Re: [Freesurfer] LME Contrasts - Longitudinal Analysis
Thanks, Martin! Sent from my iPhone > On Jan 14, 2015, at 18:34, Martin Reuter wrote: > > Hi Pedro, > > yes, the same is true for LME. > > Best, Martin > >> On 01/10/2015 04:43 PM, Pedro Rosa - Gmail wrote: >> Dear Freesurfer List, >> Reading the Wiki for the GLM procedures, I understood that that covariates >> that are “0” in the contrast matrix are “regressed out” >> (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V). >> I would like to know if this is also true for the LME contrasts >> (http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels), and if >> this applies both for categorical (e.g., gender) and continuous variables >> (e.g., age in years). >> Thank you very much in advance, >> Pedro Rosa. >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Dr. Martin Reuter > > Instructor in Neurology > Harvard Medical School > Assistant in Neuroscience > Dept. of Radiology, Massachusetts General Hospital > Dept. of Neurology, Massachusetts General Hospital > Research Affiliate > Computer Science and Artificial Intelligence Lab, > Dept. of Electrical Engineering and Computer Science, > Massachusetts Institute of Technology > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: >mreu...@nmr.mgh.harvard.edu >reu...@mit.edu > Web : http://reuter.mit.edu > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] RAM Replace
Thanks, Bruce. I am asking this because I believe that changing the processor or the operational system could change the processing. If I got it correctly, it is expected that it is not the same for the RAM. Am I correct? Thanks again, Pedro. > On Feb 23, 2015, at 21:50, Bruce Fischl wrote: > > I would very much hope that replacing the RAM wouldn't change anything > Bruce > On > Mon, 23 Feb 2015, Pedro Rosa - Gmail wrote: > >> Dear all, >> I would like to know whether a RAM memory replacement in a Mac computer >> would change >> FreeSurfer 5.3 processing. >> I have a sample that was almost completely processed, but there are a few >> subjects >> whose acquisition are yet to be done. I would like know whether I could >> process such >> images after the RAM replacement without biasing the study. The change would >> be from >> a Markvision without ECC (error-correction code) to a Kingston with ECC. >> Thanks in advance, >> Pedro Rosa. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical Misegmentation
Hi, It will upload in an hour, I guess: https://www.dropbox.com/sh/n9talmyxiafdt56/AADFttKFv3erLqDd48OpjQsna?dl=0 Thanks a lot, Pedro. > On Mar 5, 2015, at 23:32, Bruce Fischl wrote: > > Hmmm, if you upload it we will take a look > Bruce > > > >> On Mar 5, 2015, at 9:26 PM, Pedro Rosa - Gmail >> wrote: >> >> That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel size, echo >> time 5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix size 256x192mm. >> >> Pedro Rosa >> >>> On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl wrote: >>> >>> What are your acquisition parameters, voxel size etc...? >>> >>> >>> >>>> On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail >>>> wrote: >>>> >>>> Hi, Bruce. >>>> Yes, it it the T1.mgz. Is it a large topological error? Can I correct it >>>> editing wm.mgz? >>>> Thanks, >>>> Pedro. >>>>> On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote: >>>>> >>>>> What is the background image? Is it the t1 that your reconned? Can you >>>>> give us the details about it? >>>>> >>>>> >>>>> >>>>>> On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail >>>>>> wrote: >>>>>> >>>>>> Dear FreeSurfer, >>>>>> I have found several subjects to have temporal lobe misegmentations >>>>>> (usually neocortical, as attached, but sometimes mesial tempporal), and >>>>>> less frequently in the insula. >>>>>> I could find in the manual editing page from the Wiki a way to fix this. >>>>>> How should I do it? >>>>>> Thanks a lot, >>>>>> Pedro Rosa. >>>>>> >>>>>> >>>>>> ___ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> ___ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>>> >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical Misegmentation
Sure. How can I do it? Sent from my iPhone > On Mar 6, 2015, at 00:01, Bruce Fischl wrote: > > Can you put it on our ftp site instead? > > > >> On Mar 5, 2015, at 9:37 PM, Pedro Rosa wrote: >> >> Hi, >> It will upload in an hour, I guess: >> https://www.dropbox.com/sh/n9talmyxiafdt56/AADFttKFv3erLqDd48OpjQsna?dl=0 >> Thanks a lot, >> Pedro. >> >>> On Mar 5, 2015, at 23:32, Bruce Fischl wrote: >>> >>> Hmmm, if you upload it we will take a look >>> Bruce >>> >>> >>> >>>> On Mar 5, 2015, at 9:26 PM, Pedro Rosa - Gmail >>>> wrote: >>>> >>>> That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel size, echo >>>> time 5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix size >>>> 256x192mm. >>>> >>>> Pedro Rosa >>>> >>>>> On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl wrote: >>>>> >>>>> What are your acquisition parameters, voxel size etc...? >>>>> >>>>> >>>>> >>>>>> On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail >>>>>> wrote: >>>>>> >>>>>> Hi, Bruce. >>>>>> Yes, it it the T1.mgz. Is it a large topological error? Can I correct it >>>>>> editing wm.mgz? >>>>>> Thanks, >>>>>> Pedro. >>>>>>> On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote: >>>>>>> >>>>>>> What is the background image? Is it the t1 that your reconned? Can you >>>>>>> give us the details about it? >>>>>>> >>>>>>> >>>>>>> >>>>>>>> On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail >>>>>>>> wrote: >>>>>>>> >>>>>>>> Dear FreeSurfer, >>>>>>>> I have found several subjects to have temporal lobe misegmentations >>>>>>>> (usually neocortical, as attached, but sometimes mesial tempporal), >>>>>>>> and less frequently in the insula. >>>>>>>> I could find in the manual editing page from the Wiki a way to fix >>>>>>>> this. How should I do it? >>>>>>>> Thanks a lot, >>>>>>>> Pedro Rosa. >>>>>>>> >>>>>>>> >>>>>>>> ___ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> ___ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> The information in this e-mail is intended only for the person to whom >>>>>>> it is >>>>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>>>> e-mail >>>>>>> contains patient information, please contact the Partners Compliance >>>>>>> HelpLine at >>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>>>>> in error >>>>>>> but does not contain patient information, please contact the sender and >>>>>>> properly >>>>>>> dispose of the e-mail. >>>>>> >>>>>> ___ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> ___ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and
Re: [Freesurfer] Thin Surface
Hi, Bruce. I tried several thresholds in some subjects and it seems to work reallh well. Thanks for the help! However, I would like to ask whether I should determine the expert values based on the raw image (001.mgz) or the normalized image (T1.mgz)? I am asking this because I believe the normalization can change the intensity values a lot. Thanks again, Pedro. > On Feb 18, 2015, at 19:58, Bruce Fischl wrote: > > can you check mri_segmet and mris_make_surfaces and see if the auto-detected > intensity parameters are reasonable? Things like max gray at csf border and > such. If not, you can set them explicitly using the expert opts - this > usually works > Bruce >> On Wed, 18 Feb 2015, Pedro Rosa - Gmail wrote: >> >> Hi, >> I am resending it once I could not find it in the archives. >> Thanks, >> Pedro. >> >> Dear Freesurfers, >> I am working on a 1.5T MPRAGE sample of first-episode psychosis and >> controls, and have found that some subjects end up having thin cortical >> surfaces with frequent unsegmented deep sulci. I think this was worse with >> FreeSurfer 5.3 than with FreeSurfer 5.1. I attached some screen shots of >> aparc+aseg labeling T1.mgz from a few of these subjects. >> This seems to be a widespread cortical issue, although it was heterogeneous >> across subjects (some of them seemed to have the “caudal half" of both >> hemispheres adequately segmented), and trying to simply rerun those subjects >> was not very helpful. Should I manually work on them, rerun recon-all with >> distinct parameters, or just discard them? >> Regards, >> Pedro Rosa. >> >> >> >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Longitudinal - varying geometries
Hi Martin, Thank you for your answer. Is there a way to fix it? Can reslicing help? Or to try compenate for it in the processing or statistics? Regards -- Pedro Rosa > On Apr 1, 2015, at 12:13, Martin Reuter wrote: > > Hi Pedro, > > yes, there was a bug (well, not really a bug but the check was > oversensitive). It was testing too many image parameters, some of them could > be problematic (e.g. different voxel sizes across time), and some not. > > Looking at your attached files, you can see that the voxel sizes differ > significantly between the baseline and the follow-up > Baseline: > dimensions: 256 x 256 x 124 >voxel sizes: 0.8594, 0.8594, 1.5000 > Follow-up: > dimensions: 256 x 256 x 124 >voxel sizes: 1.0938, 1.0938, 1.5000 > > This can induce a bias. You need to keep imaging parameters fixed in a > longitudinal study, else you'll not know if changes are anatomical changes or > induced by the different imaging. > > Best, Martin > >> On 04/01/2015 06:43 AM, Pedro Rosa - Gmail wrote: >> Dear FreeSurfers, >> I have read in the Mailing list >> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32753.html >> and others) other users asking questioning in regard of a Warning from >> FreeSurfer 5.3 longitudinal pipeline (-base step): >> \n*** >> WARNING: Image geometries differ across time, maybe due to aquisition >> changes? >> This can potentially bias a longitudinal study! Will continue in >> 10s. >> ***\n >> I am working in a sample with a longotudinal design which receives this >> warn, although there was no change in hardware, and (supposedly) the >> acquisition protocol was the same. As requested by Martin in former posts in >> the Mailing List, I attached the output from mri_info */rawavg.mgz. >> I would like to know if these differences should be considered a bias in a >> longitudinal study and, if they should, if there is a way to fix it. >> Regards, >> Pedro Rosa. >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Dr. Martin Reuter > > Instructor in Neurology > Harvard Medical School > Assistant in Neuroscience > Dept. of Radiology, Massachusetts General Hospital > Dept. of Neurology, Massachusetts General Hospital > Research Affiliate > Computer Science and Artificial Intelligence Lab, > Dept. of Electrical Engineering and Computer Science, > Massachusetts Institute of Technology > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: >mreu...@nmr.mgh.harvard.edu >reu...@mit.edu > Web : http://reuter.mit.edu > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mris_preproc questions
Pedro Rosa Hi, I have a couple of questions about the mris_preproc: 1) Can I include all subjects in the qdec.table, but afterwards exclude some of them (based on a determined categorial variable) during the statistical analysis? I understood that the script assembles thickness / area data into a single file, but individual data is not changed depending of other subjects’ data (it assembles individual data independently of other subjects into common-space fsaverage). Am I mistaken? 2) In a longitudinal study, should I include the .base. folders in the qdec-long.table (variable 2), or is it the same to include only the .long. folders in the qdec.table (below fsid)? Thanks a lot, Pedro. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_preproc questions
Hi, 1) So I should generate a .mgh file, which will be the input for the mri_surf2surf script, for each comparison I wish to do? I have three 3 groups (schizophrenia, bipolar disorder and controls), and both schizophrenia and bipolar disorder can be further divided into remission / non-remission subgroups. If I want to compare schizophrenia subgroups to controls, not including bipolar disorder, should I run mris_preproc separately including only schizophrenia subjects and controls? 2) I intent to use de Mass-univariate model from the Linear Mixed Effects (LME) Models Wiki page. I just used the qdec.table to input the subjects list, as suggested in the Wiki. Should I necessarily include -qdec-long (table also with the .base. templates folders) in the mris_preproc or may I use the -qdec instead (including only .long. processing)? Thanks a lot! -- Pedro Rosa On Monday, January 27, 2014 at 9:07 PM, Douglas N Greve wrote: > > On 01/27/2014 06:03 PM, Pedro Rosa wrote: > > > > Pedro Rosa > > > > Hi, > > I have a couple of questions about the mris_preproc: > > 1) Can I include all subjects in the qdec.table, but afterwards exclude > > some of them (based on a determined categorial variable) during the > > statistical analysis? > > > > I don't think so. This was originally part of the plan but we never got > around to implementing it. > > I understood that the script assembles thickness / area data into a single > > file, but individual data is not changed depending of other subjects’ data > > (it assembles individual data independently of other subjects into > > common-space fsaverage). Am I mistaken? > > No, you are correct > > > > 2) In a longitudinal study, should I include the .base. folders in the > > qdec-long.table (variable 2), or is it the same to include only the .long. > > folders in the qdec.table (below fsid)? > QDEC is not the right tool for doing longitudinal analysis. Use > mri_glmfit from the command line instead. > doug > > > > > > Thanks a lot, > > Pedro. > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu (mailto:gr...@nmr.mgh.harvard.edu) > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > (http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html) > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] -noskullstrip 'directive'
Dear all, I have a dataset with 1.5T T1 images which have already been skullstriped. So to avoid the autorecon1 skullstrip, I ran 'recon-all -i subject.nii.gz -s subject -all -noskullstrip', but it finished with the same error for more than a dozen of images (example log attached). It says that the 'mri_em_register' could not open mask volume brainmask.mgz, which I believe is generated by the skullstrip and indeed could not be found in the 'subject/mri' folder. How should I ran the pipeline skipping the skullstrip? Thank you very much in advance. Pedro Rosa. recon-all.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
Dear list, I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline in a structural MRI dataset and I would like to use Monte Carlo as the method for correction for multiple comparisons. However, the longitudinal LME tutorial includes only FDR correction (lme_mass_FDR2). Is it possible to use Monte Carlo correction for longitudinal data? Can I input the outputs from MatLab (fstats = lme_mass_F(?h,CM): stats.F / pval / sgn / df) into mri_glmfit and then run Monte Carlo? If not, do you have any other suggestions of how I use Monte Carlo in longitudinal analyses? Thanks in advance, -- Pedro Rosa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
Dear Doug, Thank you very much! I will try what you suggested, although I am not sure if Jorge's stream outputs the FMHM, or if I would need to run the statistics from the beggining using in the terminal, and not in MatLab. Do you think Jorge could comment on this issue? Regards, Pedro Rosa. On Mar 24, 2014, at 12:44 PM, Douglas Greve wrote: In theory, it should be possible. I have not used Jorge's stream, so I don't know that much about it. Does it save an estimate of the FWHM? If so, then you can run mri_surfcluster passing it the p-value (ie, -log10(p)) map, the FWHM, the mask, and a voxel-wise threshold. This is what mri_glmfit-sim does, so you might check that script for mri_surfcluster command line options doug > On 3/22/14 11:03 PM, Pedro Rosa wrote: > Dear list, > I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline in a > structural MRI dataset and I would like to use Monte Carlo as the method for > correction for multiple comparisons. However, the longitudinal LME tutorial > includes only FDR correction (lme_mass_FDR2). > Is it possible to use Monte Carlo correction for longitudinal data? Can I > input the outputs from MatLab (fstats = lme_mass_F(?h,CM): stats.F / pval / > sgn / df) into mri_glmfit and then run Monte Carlo? > If not, do you have any other suggestions of how I use Monte Carlo in > longitudinal analyses? > Thanks in advance, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
Dear Doug and Jorge, Thank you very much for your help. I found another message in the list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html) in which you suggested a way of using MC in mri_glmfit-sim by creating “fake files”, which would not be read by the script. In this case, only the simulation would be run, and not the full statistics. The command would be something like this: - mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign abs I created a “fake” mri_glmfit.log, fwhm.dat and mask.mgh files as suggested by the older post. This would be fine, I believe, if only sig.mgh is read by the script. However, I get this message after running the command: [server:Long-T0-T2-Posproc/Vertex/Sch] pedrogomesrosa% mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign abs if: Expression Syntax. Is it possible to do what I am trying to do? Does the residual errors at each location included in the sig.mgh, and, if necessary, how to compute it into image FWHM? Regards, Pedro Rosa. On Friday, March 28, 2014 at 2:38 PM, Douglas N Greve wrote: > Jorge, do you output the FWHM? > doug > > On 03/27/2014 03:14 PM, jorge luis wrote: > > Hi Pedro > > > > Sorry, right now the only multiple comparisons corrections implemented > > in lme are the original Benjamini and Hochberg (1995) FDR procedure > > (lme_mass_FDR) and a more recent and powerful two-stage FDR procedure > > (lme_mass_FDR2): > > > > Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive linear > > step-up procedures that control the false discovery rate. Biometrika, > > 93, 491-507. > > > > In my experience, this procedure is as powerful to detect effects in > > neuroimage data as alternative corrections with strong control of the > > family-wise error rate (FWE). However it would be great if we could > > use an implementation of any multiple comparisons correction with > > strong control of the FWE (MC, RFT, ect...) for lme (FDR procedures > > only provide weak control). The residual errors at each location > > required to compute an estimate of the image FWHM can be obtained from > > the lme output. But an actual FWHM estimate is not currently saved. > > > > Best > > -Jorge > > > > > > El Martes 25 de marzo de 2014 8:15, Pedro Rosa > > mailto:pedrogomesr...@gmail.com)> escribió: > > > > Dear Doug, > > Thank you very much! > > I will try what you suggested, although I am not sure if Jorge's > > stream outputs the FMHM, or if I would need to run the statistics > > from the beggining using in the terminal, and not in MatLab. > > Do you think Jorge could comment on this issue? > > Regards, > > Pedro Rosa. > > > > On Mar 24, 2014, at 12:44 PM, Douglas Greve > > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > In theory, it should be possible. I have not used Jorge's stream, > > so I > > don't know that much about it. Does it save an estimate of the > > FWHM? If > > so, then you can run mri_surfcluster passing it the p-value (ie, > > -log10(p)) map, the FWHM, the mask, and a voxel-wise threshold. > > This is > > what mri_glmfit-sim does, so you might check that script for > > mri_surfcluster command line options > > > > doug > > > > > > > On 3/22/14 11:03 PM, Pedro Rosa wrote: > > > Dear list, > > > I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline > > in a structural MRI dataset and I would like to use Monte Carlo as > > the method for correction for multiple comparisons. However, the > > longitudinal LME tutorial includes only FDR correction > > (lme_mass_FDR2). > > > Is it possible to use Monte Carlo correction for longitudinal > > data? Can I input the outputs from MatLab (fstats = > > lme_mass_F(?h,CM): stats.F / pval / sgn / df) into mri_glmfit and > > then run Monte Carlo? > > > If not, do you have any other suggestions of how I use Monte > > Carlo in longitudinal analyses? > > > Thanks in advance, > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to > > whom it is > > addressed. If you believe this e-mail was sent to you in error and > > the e-mail &g
Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
Thanks, Doug! Should I run the mri_preproc and and smooth the output using mri_surf2surf with, let’s say, 10mm, and than run the LME normally in MatLab? Would this be problematic with a different smoothing procedure in mri_glmfit? How will mri_glmfit deal with the longitudinal design? Does this matter, or the FWHM would only be estimated on a average image of all time-points for all subjects? Regards, Pedro Rosa. On Sunday, March 30, 2014 at 3:51 PM, Douglas Greve wrote: > > I think I would just run mri_glmfit on your data to get the proper directly > structure and estimate of FWHM, then copy the sig file from the mixed fx > analysis into the glmfit folder for one of the contrasts. Then run > mri_glmfit-sim. > > doug > > > On 3/29/14 10:29 AM, Pedro Rosa wrote: > > Dear Doug and Jorge, > > Thank you very much for your help. > > I found another message in the list > > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html) > > in which you suggested a way of using MC in mri_glmfit-sim by creating > > “fake files”, which would not be read by the script. In this case, only the > > simulation would be run, and not the full statistics. The command would be > > something like this: > > - mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign > > abs > > I created a “fake” mri_glmfit.log, fwhm.dat and mask.mgh files as suggested > > by the older post. This would be fine, I believe, if only sig.mgh is read > > by the script. > > However, I get this message after running the command: > > [server:Long-T0-T2-Posproc/Vertex/Sch] pedrogomesrosa% mri_glmfit-sim > > --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign abs > > if: Expression Syntax. > > > > Is it possible to do what I am trying to do? Does the residual errors at > > each location included in the sig.mgh, and, if necessary, how to compute it > > into image FWHM? > > Regards, > > > > Pedro Rosa. > > > > > > On Friday, March 28, 2014 at 2:38 PM, Douglas N Greve wrote: > > > > > Jorge, do you output the FWHM? > > > doug > > > > > > On 03/27/2014 03:14 PM, jorge luis wrote: > > > > Hi Pedro > > > > > > > > Sorry, right now the only multiple comparisons corrections implemented > > > > in lme are the original Benjamini and Hochberg (1995) FDR procedure > > > > (lme_mass_FDR) and a more recent and powerful two-stage FDR procedure > > > > (lme_mass_FDR2): > > > > > > > > Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive linear > > > > step-up procedures that control the false discovery rate. Biometrika, > > > > 93, 491-507. > > > > > > > > In my experience, this procedure is as powerful to detect effects in > > > > neuroimage data as alternative corrections with strong control of the > > > > family-wise error rate (FWE). However it would be great if we could > > > > use an implementation of any multiple comparisons correction with > > > > strong control of the FWE (MC, RFT, ect...) for lme (FDR procedures > > > > only provide weak control). The residual errors at each location > > > > required to compute an estimate of the image FWHM can be obtained from > > > > the lme output. But an actual FWHM estimate is not currently saved. > > > > > > > > Best > > > > -Jorge > > > > > > > > > > > > El Martes 25 de marzo de 2014 8:15, Pedro Rosa > > > > mailto:pedrogomesr...@gmail.com)> escribió: > > > > > > > > Dear Doug, > > > > Thank you very much! > > > > I will try what you suggested, although I am not sure if Jorge's > > > > stream outputs the FMHM, or if I would need to run the statistics > > > > from the beggining using in the terminal, and not in MatLab. > > > > Do you think Jorge could comment on this issue? > > > > Regards, > > > > Pedro Rosa. > > > > > > > > On Mar 24, 2014, at 12:44 PM, Douglas Greve > > > > mailto:gr...@nmr.mgh.harvard.edu) > > > > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > > > > > > > In theory, it should be possible. I have not used Jorge's stream, > > > > so I > > > > don't know that much about it. Does it save an estimate of the > > > > FWHM? If > > > > so, then yo
Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
Dear Doug and Jorge, I tried what you suggested and I think it work, although I have some concerns.I am working with a longitudinal study with two time-points for all subjects, three categorical variables (group, substance abuse / dependence and gender) and three continuous variables (interval between scans, age and medication intake).I generated a contrast with intercept + 7 betas for the LME, ran it without any problem and saved the sig.mgh using fs_write_fstats(F_lhstats,mri,’sig.mgh’,’sig’).For the mri_glmfit I entered the same output from mri_surf2surf I used for the LME (smoothed at 10mm), but I did not know how exactly to enter the categorical and continuous variables, or which contrast to use.The commmand was: mri_glmfit —y pval.mgh —sim perm 1 0.05 schI just tested creating a matrix with 24 columns (Nclasses*(Nvariables+1) as suggested for DODS).Afterwards I ran the mri_glmfit-sim (mri_glmfit-sim --glmdir Sch-glmdir --sim mc-full 5 2 teste --sim-sign abs, and it finished apparently without errors.I attached the logs for both mri_glmfit and mri_glmfit-sim.That said, I have the following questions:1) What does the FWHM procedure does?2) How should I decide which contrast to test if the mri_glmfit does not consider the longitudinal design? 3) Will the mri_glmfit-sim consider only the FMHM output from mri_glmfit and sig.mgh from the LME, or also other outputs from the mri_glmfit?4) Does the FWHM rely only on the images, and not on variables and contrasts?Thank you very much!Pedro Rosa. On Monday, March 31, 2014 at 10:53 PM, Pedro Rosa wrote: Thanks, Doug! Should I run the mri_preproc and and smooth the output using mri_surf2surf with, let’s say, 10mm, and than run the LME normally in MatLab?Would this be problematic with a different smoothing procedure in mri_glmfit?How will mri_glmfit deal with the longitudinal design? Does this matter, or the FWHM would only be estimated on a average image of all time-points for all subjects?Regards,Pedro Rosa. On Sunday, March 30, 2014 at 3:51 PM, Douglas Greve wrote: I think I would just run mri_glmfit on your data to get the proper directly structure and estimate of FWHM, then copy the sig file from the mixed fx analysis into the glmfit folder for one of the contrasts. Then run mri_glmfit-sim. doug On 3/29/14 10:29 AM, Pedro Rosa wrote: Dear Doug and Jorge, Thank you very much for your help. I found another message in the list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html) in which you suggested a way of using MC in mri_glmfit-sim by creating “fake files”, which would not be read by the script. In this case, only the simulation would be run, and not the full statistics. The command would be something like this: - mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign abs I created a “fake” mri_glmfit.log, fwhm.dat and mask.mgh files as suggested by the older post. This would be fine, I believe, if only sig.mgh is read by the script. However, I get this message after running the command: [server:Long-T0-T2-Posproc/Vertex/Sch] pedrogomesrosa% mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign abs if: _expression_ Syntax. Is it possible to do what I am trying to do? Does the residual errors at each location included in the sig.mgh, and, if necessary, how to compute it into image FWHM? Regards, Pedro Rosa. On Friday, March 28, 2014 at 2:38 PM, Douglas N Greve wrote: Jorge, do you output the FWHM? doug On 03/27/2014 03:14 PM, jorge luis wrote: Hi Pedro Sorry, right now the only multiple comparisons corrections implemented in lme are the original Benjamini and Hochberg (1995) FDR procedure (lme_mass_FDR) and a more recent and powerful two-stage FDR procedure (lme_mass_FDR2): Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive linear step-up procedures that control the false discovery rate. Biometrika, 93, 491-507. In my
Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
Hi, Doug. Thanks a lot! The command would look like this: mri_glmfit-sim --glmdir lh.thickness.Sch.glmdir --sim mc-z 1 2 teste --sim-sign abs --overwrite --cache 1.3 abs It takes only a few seconds to run. I have a few questions about how to run it: 1) How the single entry for each subject look like in the FSGD file? 2) How to define the voxel/vertex-wise used to define clusters (after —sim, -log10( p)), and the voxel-wise threshold for the —cache option? What is the difference between them? Thanks again, Pedro Rosa. On Monday, April 14, 2014 at 3:29 PM, Douglas N Greve wrote: > > On 04/14/2014 10:35 AM, Pedro Rosa wrote: > > Dear Doug and Jorge, > > I tried what you suggested and I think it work, although I have some > > concerns. > > I am working with a longitudinal study with two time-points for all > > subjects, three categorical variables (group, substance abuse / > > dependence and gender) and three continuous variables (interval > > between scans, age and medication intake). > > I generated a contrast with intercept + 7 betas for the LME, ran it > > without any problem and saved the sig.mgh using > > fs_write_fstats(F_lhstats,mri,’sig.mgh’,’sig’). > > For the mri_glmfit I entered the same output from mri_surf2surf I used > > for the LME (smoothed at 10mm), but I did not know how exactly to > > enter the categorical and continuous variables, or which contrast to use. > > > > I would do it as a paired-test (see the wiki). You may have to re-run > mris_preproc with the --paired-diff flag, then smooth by 10mm. Use this > as the input to mri_glmfit. Set up the FSGD with the categorical and > continuous variables (note that the FSGD file will have only a single > entry per subject). Create your contrasts and run mri_glmfit. Overwrite > the sig.mgh with the one from LME. Then run mri_glmfit-sim with the > --cache option (not permutation) > > I don't know what your contrast of interest is, so I can't help you > there. In the end, it does not matter because you are overwriting the > sig map anyway. You just need a contrast as a place holder. > > doug > > > The commmand was: mri_glmfit —y pval.mgh —sim perm 1 0.05 sch > > > > I just tested creating a matrix with 24 columns > > (Nclasses*(Nvariables+1) as suggested for DODS). > > Afterwards I ran the mri_glmfit-sim (mri_glmfit-sim --glmdir > > Sch-glmdir --sim mc-full 5 2 teste --sim-sign abs, and it finished > > apparently without errors. > > I attached the logs for both mri_glmfit and mri_glmfit-sim. > > > > That said, I have the following questions: > > > > 1) What does the FWHM procedure does? > > 2) How should I decide which contrast to test if the mri_glmfit does > > not consider the longitudinal design? > > 3) Will the mri_glmfit-sim consider only the FMHM output from > > mri_glmfit and sig.mgh from the LME, or also other outputs from the > > mri_glmfit? > > 4) Does the FWHM rely only on the images, and not on variables and > > contrasts? > > > > Thank you very much! > > Pedro Rosa. > > > > On Monday, March 31, 2014 at 10:53 PM, Pedro Rosa wrote: > > > > > Thanks, Doug! > > > Should I run the mri_preproc and and smooth the output using > > > mri_surf2surf with, let’s say, 10mm, and than run the LME normally in > > > MatLab? > > > Would this be problematic with a different smoothing procedure in > > > mri_glmfit? > > > How will mri_glmfit deal with the longitudinal design? Does this > > > matter, or the FWHM would only be estimated on a average image of all > > > time-points for all subjects? > > > Regards, > > > Pedro Rosa. > > > > > > On Sunday, March 30, 2014 at 3:51 PM, Douglas Greve wrote: > > > > > > > > > > > I think I would just run mri_glmfit on your data to get the proper > > > > directly structure and estimate of FWHM, then copy the sig file from > > > > the mixed fx analysis into the glmfit folder for one of the > > > > contrasts. Then run mri_glmfit-sim. > > > > > > > > doug > > > > > > > > > > > > On 3/29/14 10:29 AM, Pedro Rosa wrote: > > > > > Dear Doug and Jorge, > > > > > Thank you very much for your help. > > > > > I found another message in the list > > > > > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html) > > > > > > > > > > in which yo
Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
Thanks, Doug! I looked at the examples on the wiki, and the Paired Analysis wiki page as well. You mentioned I should include the categorical and continuous variables in the fsgd file for the mri_glmfit. It seems that one of my analyses includes few subjects, and then one of the class end up lacking a adequate range of continuous variables, and consequently the mri_glmfit finished with errors (this error no longer appears after I merged that problematic group with another). Therefore I ask whether it would be fine to run the mri_glmfit without some (or all) the continuous or/an categorical variables, while they would of course be included in the LME ran in MatLab. Further, I would like to ask what the FMHM outputs represents? Regards, Pedro Rosa. On Wednesday, April 16, 2014 at 11:49 AM, Douglas N Greve wrote: > > On 04/15/2014 10:34 PM, Pedro Rosa wrote: > > Hi, Doug. > > Thanks a lot! > > The command would look like this: mri_glmfit-sim --glmdir > > lh.thickness.Sch.glmdir --sim mc-z 1 2 teste --sim-sign abs > > --overwrite --cache 1.3 abs > > It takes only a few seconds to run. > > > > The command is fine, but remove --sim mc-z 1 2 teste. This tells it > to do the simulation, which you don't need to do. It is overridden by > the --cache flag. If they had occurred in the other order, you would be > waiting days for the simulation to run. > > I have a few questions about how to run it: > > 1) How the single entry for each subject look like in the FSGD file? > > > > I'm not sure what you mean. Have you looked at the examples on the wiki? > > > > 2) How to define the voxel/vertex-wise used to define clusters (after > > —sim, -log10( p)), and the voxel-wise threshold for the —cache option? > > What is the difference between them? > > > > They are the same > doug > > > > Thanks again, > > Pedro Rosa. > > > > On Monday, April 14, 2014 at 3:29 PM, Douglas N Greve wrote: > > > > > > > > On 04/14/2014 10:35 AM, Pedro Rosa wrote: > > > > Dear Doug and Jorge, > > > > I tried what you suggested and I think it work, although I have some > > > > concerns. > > > > I am working with a longitudinal study with two time-points for all > > > > subjects, three categorical variables (group, substance abuse / > > > > dependence and gender) and three continuous variables (interval > > > > between scans, age and medication intake). > > > > I generated a contrast with intercept + 7 betas for the LME, ran it > > > > without any problem and saved the sig.mgh using > > > > fs_write_fstats(F_lhstats,mri,’sig.mgh’,’sig’). > > > > For the mri_glmfit I entered the same output from mri_surf2surf I used > > > > for the LME (smoothed at 10mm), but I did not know how exactly to > > > > enter the categorical and continuous variables, or which contrast to > > > > use. > > > > > > > > > > I would do it as a paired-test (see the wiki). You may have to re-run > > > mris_preproc with the --paired-diff flag, then smooth by 10mm. Use this > > > as the input to mri_glmfit. Set up the FSGD with the categorical and > > > continuous variables (note that the FSGD file will have only a single > > > entry per subject). Create your contrasts and run mri_glmfit. Overwrite > > > the sig.mgh with the one from LME. Then run mri_glmfit-sim with the > > > --cache option (not permutation) > > > > > > I don't know what your contrast of interest is, so I can't help you > > > there. In the end, it does not matter because you are overwriting the > > > sig map anyway. You just need a contrast as a place holder. > > > > > > doug > > > > > > > The commmand was: mri_glmfit —y pval.mgh —sim perm 1 0.05 sch > > > > > > > > I just tested creating a matrix with 24 columns > > > > (Nclasses*(Nvariables+1) as suggested for DODS). > > > > Afterwards I ran the mri_glmfit-sim (mri_glmfit-sim --glmdir > > > > Sch-glmdir --sim mc-full 5 2 teste --sim-sign abs, and it finished > > > > apparently without errors. > > > > I attached the logs for both mri_glmfit and mri_glmfit-sim. > > > > > > > > That said, I have the following questions: > > > > > > > > 1) What does the FWHM procedure does? > > > > 2) How should I decide which contrast to test if the mri_glmfit does > > > > not consider the longitudinal design? > > > > 3) Wi
Re: [Freesurfer] FWHM file not found
Thanks for que quick answer, Marie. If I got right, I should either not smooth it after mri_preproc (no mri_surf2surf) or do it with kernels < 5mm, and that should make to FMHM fall below 30. Am I correct? Thanks, Pedro. On Wed, Mar 16, 2016 at 3:03 PM, Marie Schaer wrote: > > Hi Pedro, > > So lGI is inherently very smoothed, and you don’t want to over smooth > (which is why you get this error), so I usually recommend either no > smoothing (fwhm=0) or fwhm=5mm, given that these are the options easily > inputed in qdec. I’d say try first with 5mm, and check if this work, if it > doesn't decrease to 0mm. And if you want then to work around, you can tune > your smoothing with values in between to achieve a smoothness level of > 15mm, most often with 1 or 2mm, but qdec won’t accept it so you’ll have to > go for the commandline stats. > > Hope it helps, > > Marie > > > > > > > On 16 Mar 2016, at 10:50, Pedro Rosa wrote: > > > > Dear FreeSurfers, > > I am running a localgi analysis using mri_glmfit and mri_glmfit-sim, and > it seems the last script looked for > freesurfer/average/mult-comp-cor/fsaverage/?h/cortex/fwhm40/abs/th13/mc-z.cdf > and mc-z.csd, but there are precached data until fmhm30. > > How should I proceed? > > Best, > > Pedro. > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom > it is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FWHM file not found
Dear FreeSurfers, I am running a localgi analysis using mri_glmfit and mri_glmfit-sim, and it seems the last script looked for freesurfer/average/mult-comp-cor/fsaverage/?h/cortex/fwhm40/abs/th13/mc-z.cdf and mc-z.csd, but there are precached data until fmhm30. How should I proceed? Best, Pedro. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] glmfit and glmfit-sim after built monte-carlo simulation (superiortemporal label)
Dear list, I want to limit my vertex-wise group analysis to a smaller spatial region, then I ran my own Monte-Carlo simulation on fsaverage for the superior temporal gyrus: mri_mcsim --o lh/superiortemporal --base mc-z --surface /fsaverage lh --nreps 1 --label superiortemporal After 36 hours, it finished and I pasted the resulting into $FREESURFER_HOME/average/mult-comp-cor/fsaverage, and ran glmfit: mri_glmfit --glmdir glmdir --y lh.thickness.5.mgh --fsgd table.fsgd --C contrast.mtx --surface fsaverage lh --label /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label It seems it ran only on the label, as expected. However I am not able touse this pre-cached simulation in mri_glmfit-sim. I tried: mri_glmfit-sim --glmdir glmdir --sim-sign abs --cache-dir $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/superiortemporal --no-sim mc-z.abs.th13 --cache-label /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label ...but I get an error although the csd files are in /average/mult-comp-cor/fsaverage... path : ERROR: cannot find any csd files I tried several combinations of the text specified after --no-sim, but all I got is the error above. I though I should refer to my own simulation using --cache-dir, but it requires the --no-sim flag. Can anyone help me? Best, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] glmfit and glmfit-sim after built monte-carlo simulation (superiortemporal label)
Thanks, Doug. When I do it, I get the following error: ERROR: must spec --sim I am using FreeSurfer 5.3 in a Mac OS. I read in the wiki that mri_mcsim got an atualization for Linux. Should I get that atualization for Mac Os? Best, Pedro. On Wed, Apr 13, 2016 at 11:43 AM, Douglas Greve wrote: > Try it without the --no-sim. The --no-sim was from before I stored the > cached data and you either had to run a simulation or not. > > > On 4/12/16 9:10 PM, Pedro Rosa wrote: > > Dear list, > I want to limit my vertex-wise group analysis to a smaller spatial region, > then I ran my own Monte-Carlo simulation on fsaverage for the superior > temporal gyrus: > > mri_mcsim --o lh/superiortemporal --base mc-z --surface /fsaverage lh > --nreps 1 --label superiortemporal > > > After 36 hours, it finished and I pasted the resulting into > $FREESURFER_HOME/average/mult-comp-cor/fsaverage, and > ran glmfit: > > mri_glmfit --glmdir glmdir --y lh.thickness.5.mgh --fsgd table.fsgd --C > contrast.mtx --surface fsaverage lh --label > /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label > > It seems it ran only on the label, as expected. > > However I am not able touse this pre-cached simulation in mri_glmfit-sim. > > I tried: mri_glmfit-sim --glmdir glmdir --sim-sign abs --cache-dir > $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/superiortemporal > --no-sim mc-z.abs.th13 --cache-label > /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label > > > ...but I get an error although the csd files are in > /average/mult-comp-cor/fsaverage... path : ERROR: cannot find any csd > files > > I tried several combinations of the text specified after --no-sim, but all > I got is the error above. I though I should refer to my own simulation > using --cache-dir, but it requires the --no-sim flag. > > Can anyone help me? > > Best, > > Pedro Rosa. > > > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] glmfit and glmfit-sim after built monte-carlo simulation (superiortemporal label)
Hi, Many many thanks. It worked: mri_glmfit-sim --glmdir teste2 --cache-dir /$FREESURFER_HOME/average/mult-comp-cor/ --cache 1.3 abs --cache-label superiortemporal I had so specify --cache-label as well, or it would try to find the default fsaverage/cortex label. The summary table is named as the deafault ones (cache.th13.abs.sig.cluster.summary), but I found this in it: # SearchSpace_mm2 65416.6 ## against 65020.8 for deafult ones # SearchSpace_vtx 7271 ## against 149926 for default ones Does this mean that both GLM and Monte-Carlo ran in the label exclusively? By the way, no cluster survived the correction. Best, Pedro. On Thu, Apr 14, 2016 at 6:49 PM, Douglas N Greve wrote: > You will need to also specify a voxel-wise threshold and sign, eg, > > --cache 2 abs > > > > On 04/13/2016 07:37 PM, Pedro Rosa wrote: > > Thanks, Doug. > > When I do it, I get the following error: ERROR: must spec --sim > > I am using FreeSurfer 5.3 in a Mac OS. I read in the wiki that > > mri_mcsim got an atualization for Linux. Should I get that > > atualization for Mac Os? > > Best, > > Pedro. > > > > On Wed, Apr 13, 2016 at 11:43 AM, Douglas Greve > > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > Try it without the --no-sim. The --no-sim was from before I stored > > the cached data and you either had to run a simulation or not. > > > > > > On 4/12/16 9:10 PM, Pedro Rosa wrote: > >> Dear list, > >> I want to limit my vertex-wise group analysis to a smaller > >> spatial region, then I ran my own Monte-Carlo simulation on > >> fsaverage for the superior temporal gyrus: > >> > >> mri_mcsim --o lh/superiortemporal --base mc-z --surface > >> /fsaverage lh --nreps 1 --label superiortemporal > >> > >> > >> After 36 hours, it finished and I pasted the resulting into > >> $FREESURFER_HOME/average/mult-comp-cor/fsaverage, and ran glmfit: > >> > >> mri_glmfit --glmdir glmdir --y lh.thickness.5.mgh --fsgd > >> table.fsgd --C contrast.mtx --surface fsaverage lh --label > >> /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label > >> > >> It seems it ran only on the label, as expected. > >> > >> However I am not able touse this pre-cached simulation in > >> mri_glmfit-sim. > >> > >> I tried: mri_glmfit-sim --glmdir glmdir --sim-sign abs > >> --cache-dir > >> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/superiortemporal > >> --no-sim mc-z.abs.th13 --cache-label > >> /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label > >> > >> > >> ...but I get an error although the csd files are in > >> /average/mult-comp-cor/fsaverage... path : ERROR: cannot find any > >> csd files > >> > >> I tried several combinations of the text specified after > >> --no-sim, but all I got is the error above. I though I should > >> refer to my own simulation using --cache-dir, but it requires the > >> --no-sim flag. > >> > >> Can anyone help me? > >> > >> Best, > >> > >> Pedro Rosa. > >> > >> > >> > >> > >> > >> ___ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to > > whom it is > > addressed. If you believe this e-mail was sent to you in error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.
[Freesurfer] glmfit --table (by tract TRACULA outputs)
Dear list, I am trying to use mri_glmfit to run statistics on TRACULA outputs (by tract), as suggested by the wiki ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics). I used the following command line: mri_glmfit --glmdir ilf.glmdir --table ilf.txt --fsgd sociodemo.fsgd --C 2G1V-1100.mtx It ends without errors. How should I proceed with correction for multiple comparisons, as I cannot use Monte Carlo? Best, Pedro. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] GLM - covariate question
Dear list, I am running a command line group analysis, and I want to include a covariate that is zero for all subjects in a group, and diverse for all subjects in the second group (medication intake, which is null for all subjects in the control group). This generates a lack of range of that continuous variable within a class (control group), and thus mri_glmfit ends with errors. Is it possible to perform such analysis? Could demeaning procedure work here? If not, how could I "regress out" the effect of such covariate in between-groups thickness/area differences? Many thanks in advance, Pedro. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] GLM - covariate question
Dear Donald, Thank you very much for the explanation. I have found much trouble in modeling my data, and you are already helping a lot! I believe the "medication problem" is very hard to solve, but perhaps one or two models can be useful although reliant on a few more premisses. Without them, it would be impossible to attribute group differences to a "diagnosis" if only patients received a certain type of medication. If I got it correctly, using a DOSS model would assume that the slope for medication (covariate) in the controls (unknown, as no control received it) is the same as the patients' slope for medication (known). This is a very strong biological assumption, I know. Another option would be to use a DOSS / DODS (if the patients group is divided, let's say, by gender) model excluding the controls. Am I following your thoughts here? Best, Pedro. On Mon, May 9, 2016 at 10:15 PM, MCLAREN, Donald wrote: > Pedro, > > Instead of saying that you want to include the covariate in the analysis, > it's better to consider why you want to include the covariate and how it > changes the interpretation. You don't necessarily want to regress out > covariates, especially when the covariate is different between groups. > > DO -- Different offsets, no covariate/no slope --> the offsets are the > group means not adjusted for covariates. > DOSS -- Different offset, same slope model --> If you don't subtract the > mean, then the offsets are the group means when the covariate is 0 for all > subjects. If you subtract the mean, then the offsets are the group means > when the the covariate is the mean covariate for all subjects. The > difference in offsets won't change with mean centering the covariate. > DODS -- Different offset, different slope model --> Not possible because > the covariate for controls is collinear with the group term. > > There are other models that you could construct - such as only including a > covariate for the drug group, but the interpretation will once again be > different. > > The bottom line is to decide what you want to test and how you want to > interpret the results before adding covariates. > With DOSS, you will reduce/increase the group differences (depending on > the slope of the covariate) because you are interpreting the results when > the covariate is 0 in the drug group. > > Best, > Donald > > > Best Regards, > Donald McLaren, PhD > > > On Sat, May 7, 2016 at 3:18 PM, Pedro Rosa > wrote: > >> Dear list, >> I am running a command line group analysis, and I want to include a >> covariate that is zero for all subjects in a group, and diverse for all >> subjects in the second group (medication intake, which is null for all >> subjects in the control group). >> This generates a lack of range of that continuous variable within a class >> (control group), and thus mri_glmfit ends with errors. >> Is it possible to perform such analysis? Could demeaning procedure work >> here? >> If not, how could I "regress out" the effect of such covariate in >> between-groups thickness/area differences? >> Many thanks in advance, >> Pedro. >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Local GI - longitudinal analysis
Dear all, I have two issues: 1) I would like to run localGI in a longitudinal analysis. I runned the recon-all, the -base and the -long in all subjects. Then, I tried to run the -localGI command on .long. directories (I believe this it the directory I should run the command), the error below returned. How can I solve this issue? 2) I tried to download the 5.2 version, but the link does not seem to be working (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/). I tried both Chrome and Firefox. Regards, Pedro Rosa. ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters: \' -long \' where is the time point id (SAME as cross sectional ID) and is the ID created in the -base run. The directory .long. will be created automatically or used for output, if it already exists.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] wmparc.mgz
Hi, Is it possible to obtain the wmparc.mgz file without running all steps from autorecon2 and 3? Thanks, Pedro. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR
Hi, Sorry for that! I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target Thank you again, Pedro Rosa On 20 Aug 2013, at 12:34 PM, Douglas N Greve wrote: > They should be fine. BTW, you can run > > recon-all -s subject -make all > > and it will only run the parts that need to be run > > doug > > > On 08/20/2013 12:13 PM, Pedro Rosa wrote: >> Hi, >> I am mainly interested in using the wmparc.mgz files. Are they alright in >> the subjects with this error in autorecon2? It would be better if I could >> use this processing, as doing it again in 80 subjects would take a lot of >> time. Autorecon 1 and 3 ended without errors for all subjects. I inspected >> the wmparc.mgz files as labels using Slicer 4, and they seem fine. >> Thanks, >> Pedro Rosa. >> >> On 20 Aug 2013, at 10:28 AM, Douglas N Greve >> wrote: >> >>> Hi Pedro, see the release notes for the issue >>> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >>> doug >>> >>> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>>> Hi experts, >>>> I am processing several subjects, and they all ended up with the same >>>> error at the autorecon2: ribbon.mgz could not be opened. I ran at first >>>> the autorecon1 to check the skull striping, and then autorecon2 and 3. >>>> Autorecon3 always finished without error. I attached a log file. >>>> >>>> >>>> Any help is appreciated. >>>> Regards, >>>> Pedro Rosa. >>>> >>>> >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR
Hi, I tried using several targets: all / autorecon1-2-3, and for all I get 'make: command not found.' I used recon-all -s subject -make target Pedro Rosa On 20 Aug 2013, at 12:34 PM, Douglas N Greve wrote: > They should be fine. BTW, you can run > > recon-all -s subject -make all > > and it will only run the parts that need to be run > > doug > > > On 08/20/2013 12:13 PM, Pedro Rosa wrote: >> Hi, >> I am mainly interested in using the wmparc.mgz files. Are they alright in >> the subjects with this error in autorecon2? It would be better if I could >> use this processing, as doing it again in 80 subjects would take a lot of >> time. Autorecon 1 and 3 ended without errors for all subjects. I inspected >> the wmparc.mgz files as labels using Slicer 4, and they seem fine. >> Thanks, >> Pedro Rosa. >> >> On 20 Aug 2013, at 10:28 AM, Douglas N Greve >> wrote: >> >>> Hi Pedro, see the release notes for the issue >>> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >>> doug >>> >>> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>>> Hi experts, >>>> I am processing several subjects, and they all ended up with the same >>>> error at the autorecon2: ribbon.mgz could not be opened. I ran at first >>>> the autorecon1 to check the skull striping, and then autorecon2 and 3. >>>> Autorecon3 always finished without error. I attached a log file. >>>> >>>> >>>> Any help is appreciated. >>>> Regards, >>>> Pedro Rosa. >>>> >>>> >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR
Hi, I could not find the make file. I am using Mac OS (most recent). Thanks Pedro Rosa On 21 Aug 2013, at 10:51 AM, Douglas N Greve wrote: > > You will need to add the "make" program to your path. In Linux, it is > usually in /usr/bin > doug > > > On 08/20/2013 10:12 PM, Pedro Rosa wrote: >> Hi, >> Sorry for that! >> I tried using several targets: all / autorecon1-2-3, and for all I get >> 'make: command not found.' >> I used recon-all -s subject -make target >> Thank you again, >> Pedro Rosa >> >> On 20 Aug 2013, at 12:34 PM, Douglas N Greve >> wrote: >> >>> They should be fine. BTW, you can run >>> >>> recon-all -s subject -make all >>> >>> and it will only run the parts that need to be run >>> >>> doug >>> >>> >>> On 08/20/2013 12:13 PM, Pedro Rosa wrote: >>>> Hi, >>>> I am mainly interested in using the wmparc.mgz files. Are they alright in >>>> the subjects with this error in autorecon2? It would be better if I could >>>> use this processing, as doing it again in 80 subjects would take a lot of >>>> time. Autorecon 1 and 3 ended without errors for all subjects. I inspected >>>> the wmparc.mgz files as labels using Slicer 4, and they seem fine. >>>> Thanks, >>>> Pedro Rosa. >>>> >>>> On 20 Aug 2013, at 10:28 AM, Douglas N Greve >>>> wrote: >>>> >>>>> Hi Pedro, see the release notes for the issue >>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >>>>> doug >>>>> >>>>> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>>>>> Hi experts, >>>>>> I am processing several subjects, and they all ended up with the same >>>>>> error at the autorecon2: ribbon.mgz could not be opened. I ran at first >>>>>> the autorecon1 to check the skull striping, and then autorecon2 and 3. >>>>>> Autorecon3 always finished without error. I attached a log file. >>>>>> >>>>>> >>>>>> Any help is appreciated. >>>>>> Regards, >>>>>> Pedro Rosa. >>>>>> >>>>>> >>>>>> ___ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> gr...@nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> ___ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom it >>>>> is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>>> error >>>>> but does not contain patient information, please contact the sender and >>>>> properly >>>>> dispose of the e-mail. >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR
Hi, I use two Macs. One with OS X 10.8.4 and one with OS X 10.8.3. I suppose that if the problem is with the mri_segstats the wmparc.mgz should not have been affected. I am correct? However, if I want to extract stats from volumetry/surface perhaps I will find myself in trouble. Pedro Rosa On 21 Aug 2013, at 12:33 PM, Douglas N Greve wrote: > > Yea, I don't think mac os comes with it by default. If you want to use > this functionality, you'll have to install it. Zeke, can you point him > in the right direction? > > to get back to your original problem, I think I gave you the wrong > version of mri_segstats. What version of mac os do you have? If I get > you the right version, then you might not need the make option. > > doug > > > On 08/21/2013 12:06 PM, Pedro Rosa wrote: >> Hi, >> I could not find the make file. I am using Mac OS (most recent). >> Thanks >> >> Pedro Rosa >> >> On 21 Aug 2013, at 10:51 AM, Douglas N Greve >> wrote: >> >>> You will need to add the "make" program to your path. In Linux, it is >>> usually in /usr/bin >>> doug >>> >>> >>> On 08/20/2013 10:12 PM, Pedro Rosa wrote: >>>> Hi, >>>> Sorry for that! >>>> I tried using several targets: all / autorecon1-2-3, and for all I get >>>> 'make: command not found.' >>>> I used recon-all -s subject -make target >>>> Thank you again, >>>> Pedro Rosa >>>> >>>> On 20 Aug 2013, at 12:34 PM, Douglas N Greve >>>> wrote: >>>> >>>>> They should be fine. BTW, you can run >>>>> >>>>> recon-all -s subject -make all >>>>> >>>>> and it will only run the parts that need to be run >>>>> >>>>> doug >>>>> >>>>> >>>>> On 08/20/2013 12:13 PM, Pedro Rosa wrote: >>>>>> Hi, >>>>>> I am mainly interested in using the wmparc.mgz files. Are they alright >>>>>> in the subjects with this error in autorecon2? It would be better if I >>>>>> could use this processing, as doing it again in 80 subjects would take a >>>>>> lot of time. Autorecon 1 and 3 ended without errors for all subjects. I >>>>>> inspected the wmparc.mgz files as labels using Slicer 4, and they seem >>>>>> fine. >>>>>> Thanks, >>>>>> Pedro Rosa. >>>>>> >>>>>> On 20 Aug 2013, at 10:28 AM, Douglas N Greve >>>>>> wrote: >>>>>> >>>>>>> Hi Pedro, see the release notes for the issue >>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >>>>>>> doug >>>>>>> >>>>>>> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>>>>>>> Hi experts, >>>>>>>> I am processing several subjects, and they all ended up with the same >>>>>>>> error at the autorecon2: ribbon.mgz could not be opened. I ran at >>>>>>>> first the autorecon1 to check the skull striping, and then autorecon2 >>>>>>>> and 3. Autorecon3 always finished without error. I attached a log file. >>>>>>>> >>>>>>>> >>>>>>>> Any help is appreciated. >>>>>>>> Regards, >>>>>>>> Pedro Rosa. >>>>>>>> >>>>>>>> >>>>>>>> ___ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> gr...@nmr.mgh.harvard.edu >>>>>>> Phone Number: 617-724-2358 >>>>>>> Fax: 617-726-7422 >>>>>>> >>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>> >>>>>>> ___
Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR
Both are mountain lion. Pedro Rosa On 21 Aug 2013, at 01:11 PM, Douglas N Greve wrote: > > right the wmparc.mgz is not affected. Is your mac mountainlion or leopard or > snowleopard? > > > On 08/21/2013 01:05 PM, Pedro Rosa wrote: >> Hi, >> I use two Macs. One with OS X 10.8.4 and one with OS X 10.8.3. >> I suppose that if the problem is with the mri_segstats the wmparc.mgz should >> not have been affected. I am correct? However, if I want to extract stats >> from volumetry/surface perhaps I will find myself in trouble. >> >> Pedro Rosa >> >> On 21 Aug 2013, at 12:33 PM, Douglas N Greve >> wrote: >> >>> Yea, I don't think mac os comes with it by default. If you want to use >>> this functionality, you'll have to install it. Zeke, can you point him >>> in the right direction? >>> >>> to get back to your original problem, I think I gave you the wrong >>> version of mri_segstats. What version of mac os do you have? If I get >>> you the right version, then you might not need the make option. >>> >>> doug >>> >>> >>> On 08/21/2013 12:06 PM, Pedro Rosa wrote: >>>> Hi, >>>> I could not find the make file. I am using Mac OS (most recent). >>>> Thanks >>>> >>>> Pedro Rosa >>>> >>>> On 21 Aug 2013, at 10:51 AM, Douglas N Greve >>>> wrote: >>>> >>>>> You will need to add the "make" program to your path. In Linux, it is >>>>> usually in /usr/bin >>>>> doug >>>>> >>>>> >>>>> On 08/20/2013 10:12 PM, Pedro Rosa wrote: >>>>>> Hi, >>>>>> Sorry for that! >>>>>> I tried using several targets: all / autorecon1-2-3, and for all I get >>>>>> 'make: command not found.' >>>>>> I used recon-all -s subject -make target >>>>>> Thank you again, >>>>>> Pedro Rosa >>>>>> >>>>>> On 20 Aug 2013, at 12:34 PM, Douglas N Greve >>>>>> wrote: >>>>>> >>>>>>> They should be fine. BTW, you can run >>>>>>> >>>>>>> recon-all -s subject -make all >>>>>>> >>>>>>> and it will only run the parts that need to be run >>>>>>> >>>>>>> doug >>>>>>> >>>>>>> >>>>>>> On 08/20/2013 12:13 PM, Pedro Rosa wrote: >>>>>>>> Hi, >>>>>>>> I am mainly interested in using the wmparc.mgz files. Are they alright >>>>>>>> in the subjects with this error in autorecon2? It would be better if I >>>>>>>> could use this processing, as doing it again in 80 subjects would take >>>>>>>> a lot of time. Autorecon 1 and 3 ended without errors for all >>>>>>>> subjects. I inspected the wmparc.mgz files as labels using Slicer 4, >>>>>>>> and they seem fine. >>>>>>>> Thanks, >>>>>>>> Pedro Rosa. >>>>>>>> >>>>>>>> On 20 Aug 2013, at 10:28 AM, Douglas N Greve >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi Pedro, see the release notes for the issue >>>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >>>>>>>>> doug >>>>>>>>> >>>>>>>>> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>>>>>>>>> Hi experts, >>>>>>>>>> I am processing several subjects, and they all ended up with the >>>>>>>>>> same error at the autorecon2: ribbon.mgz could not be opened. I ran >>>>>>>>>> at first the autorecon1 to check the skull striping, and then >>>>>>>>>> autorecon2 and 3. Autorecon3 always finished without error. I >>>>>>>>>> attached a log file. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Any help is appreciated. >>>>>>>>>> Regards, >>>>>>>>>> Pedro Rosa. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>&g
Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR
Hi, Thank you. It seems to be working. The command returns, however, that there is nothing to be done in all three autorecons individually. What should that mean, considering the error in autorecon2? Regards Pedro Rosa On 21 Aug 2013, at 04:16 PM, Z K wrote: > Getting 'make' on Mac systems requires installing XCode AND Command Line > Tool. You can download these from Apple using the following link: > > https://developer.apple.com/downloads > > FYI: This will require opening a developer account (free) if you do not > already have one. > > -Zeke > > > > On 08/21/2013 12:33 PM, Douglas N Greve wrote: >> >> Yea, I don't think mac os comes with it by default. If you want to use >> this functionality, you'll have to install it. Zeke, can you point him >> in the right direction? >> >> to get back to your original problem, I think I gave you the wrong >> version of mri_segstats. What version of mac os do you have? If I get >> you the right version, then you might not need the make option. >> >> doug >> >> >> On 08/21/2013 12:06 PM, Pedro Rosa wrote: >>> Hi, >>> I could not find the make file. I am using Mac OS (most recent). >>> Thanks >>> >>> Pedro Rosa >>> >>> On 21 Aug 2013, at 10:51 AM, Douglas N Greve >>> wrote: >>> >>>> You will need to add the "make" program to your path. In Linux, it is >>>> usually in /usr/bin >>>> doug >>>> >>>> >>>> On 08/20/2013 10:12 PM, Pedro Rosa wrote: >>>>> Hi, >>>>> Sorry for that! >>>>> I tried using several targets: all / autorecon1-2-3, and for all I get >>>>> 'make: command not found.' >>>>> I used recon-all -s subject -make target >>>>> Thank you again, >>>>> Pedro Rosa >>>>> >>>>> On 20 Aug 2013, at 12:34 PM, Douglas N Greve >>>>> wrote: >>>>> >>>>>> They should be fine. BTW, you can run >>>>>> >>>>>> recon-all -s subject -make all >>>>>> >>>>>> and it will only run the parts that need to be run >>>>>> >>>>>> doug >>>>>> >>>>>> >>>>>> On 08/20/2013 12:13 PM, Pedro Rosa wrote: >>>>>>> Hi, >>>>>>> I am mainly interested in using the wmparc.mgz files. Are they alright >>>>>>> in the subjects with this error in autorecon2? It would be better if I >>>>>>> could use this processing, as doing it again in 80 subjects would take >>>>>>> a lot of time. Autorecon 1 and 3 ended without errors for all subjects. >>>>>>> I inspected the wmparc.mgz files as labels using Slicer 4, and they >>>>>>> seem fine. >>>>>>> Thanks, >>>>>>> Pedro Rosa. >>>>>>> >>>>>>> On 20 Aug 2013, at 10:28 AM, Douglas N Greve >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Pedro, see the release notes for the issue >>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >>>>>>>> doug >>>>>>>> >>>>>>>> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>>>>>>>> Hi experts, >>>>>>>>> I am processing several subjects, and they all ended up with the same >>>>>>>>> error at the autorecon2: ribbon.mgz could not be opened. I ran at >>>>>>>>> first the autorecon1 to check the skull striping, and then autorecon2 >>>>>>>>> and 3. Autorecon3 always finished without error. I attached a log >>>>>>>>> file. >>>>>>>>> >>>>>>>>> >>>>>>>>> Any help is appreciated. >>>>>>>>> Regards, >>>>>>>>> Pedro Rosa. >>>>>>>>> >>>>>>>>> >>>>>>>>> ___ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> -- >>>>>>>&
Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR
For now I only need brainmask.mgz and wmparc.mgz, so Yes. In case I need other files in the future (i.e. mri_segstats) I plan to run all processing again. Thanks a lot! Pedro Rosa On 23 Aug 2013, at 11:36 AM, Douglas N Greve wrote: > > Are all the files you need there? If not, what is missing? > > > > On 08/22/2013 07:41 PM, Pedro Rosa wrote: >> Hi, >> Thank you. It seems to be working. The command returns, however, that there >> is nothing to be done in all three autorecons individually. What should that >> mean, considering the error in autorecon2? >> Regards >> >> Pedro Rosa >> >> On 21 Aug 2013, at 04:16 PM, Z K wrote: >> >>> Getting 'make' on Mac systems requires installing XCode AND Command Line >>> Tool. You can download these from Apple using the following link: >>> >>> https://developer.apple.com/downloads >>> >>> FYI: This will require opening a developer account (free) if you do not >>> already have one. >>> >>> -Zeke >>> >>> >>> >>> On 08/21/2013 12:33 PM, Douglas N Greve wrote: >>>> Yea, I don't think mac os comes with it by default. If you want to use >>>> this functionality, you'll have to install it. Zeke, can you point him >>>> in the right direction? >>>> >>>> to get back to your original problem, I think I gave you the wrong >>>> version of mri_segstats. What version of mac os do you have? If I get >>>> you the right version, then you might not need the make option. >>>> >>>> doug >>>> >>>> >>>> On 08/21/2013 12:06 PM, Pedro Rosa wrote: >>>>> Hi, >>>>> I could not find the make file. I am using Mac OS (most recent). >>>>> Thanks >>>>> >>>>> Pedro Rosa >>>>> >>>>> On 21 Aug 2013, at 10:51 AM, Douglas N Greve >>>>> wrote: >>>>> >>>>>> You will need to add the "make" program to your path. In Linux, it is >>>>>> usually in /usr/bin >>>>>> doug >>>>>> >>>>>> >>>>>> On 08/20/2013 10:12 PM, Pedro Rosa wrote: >>>>>>> Hi, >>>>>>> Sorry for that! >>>>>>> I tried using several targets: all / autorecon1-2-3, and for all I get >>>>>>> 'make: command not found.' >>>>>>> I used recon-all -s subject -make target >>>>>>> Thank you again, >>>>>>> Pedro Rosa >>>>>>> >>>>>>> On 20 Aug 2013, at 12:34 PM, Douglas N Greve >>>>>>> wrote: >>>>>>> >>>>>>>> They should be fine. BTW, you can run >>>>>>>> >>>>>>>> recon-all -s subject -make all >>>>>>>> >>>>>>>> and it will only run the parts that need to be run >>>>>>>> >>>>>>>> doug >>>>>>>> >>>>>>>> >>>>>>>> On 08/20/2013 12:13 PM, Pedro Rosa wrote: >>>>>>>>> Hi, >>>>>>>>> I am mainly interested in using the wmparc.mgz files. Are they >>>>>>>>> alright in the subjects with this error in autorecon2? It would be >>>>>>>>> better if I could use this processing, as doing it again in 80 >>>>>>>>> subjects would take a lot of time. Autorecon 1 and 3 ended without >>>>>>>>> errors for all subjects. I inspected the wmparc.mgz files as labels >>>>>>>>> using Slicer 4, and they seem fine. >>>>>>>>> Thanks, >>>>>>>>> Pedro Rosa. >>>>>>>>> >>>>>>>>> On 20 Aug 2013, at 10:28 AM, Douglas N Greve >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hi Pedro, see the release notes for the issue >>>>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >>>>>>>>>> doug >>>>>>>>>> >>>>>>>>>> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>>>>>>>>>> Hi experts, >>>>>>>>>>> I am processing several subjects, and th
[Freesurfer] Could not find .mat
Hi, I am finding a warning at recon-all when creating the folders: INFO: could not find /Path/subject.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 1, coronal unflipped. INFO: if not valid, please provide the information in /Path/subject.mat file What are the consequences of this to image orientation or to registration in further steps? I have sorted the DICOMs using MRIcron (generates .img and .hdr for T1 acquisition). Regards, Pedro. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Skull Striping
Dear all, I am currently working on a 1.5T SPGR 1.5mm MRI longitudinal dataset, and I would like to know if one is expected to manually skull strip the images before de recon -all procedure. I am aware that the image quality may be a limiting factor for the freesurfer processing. Regards, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Contrast interpretation - between-groups mean
External Email - Use Caution Dear FreeSurfers, I got results from a cortical area analysis that intrigued me: Upon the inspection of clusters that survived Monte-Carlo simulation, I found a cluster with larger area among a first group in contrast to a second group. However, when I calculated the cortical areas means from that cluster (as available in the glmdir), the second group had values slightly larger than the first group (i.e., showing a difference in the opposite direction). How would you explain such findings? Must I have committed a mistake in the analysis or its interpretation? Best, Pedro Rosa - University of São Paulo - Brazil. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Contrast interpretation - between-groups mean
External Email - Use Caution Hi, Doug. Many thanks. Find the fsgd and the contrast attached, as well as the cluster summary and the individual-based cluster data (which I used to calculate the groups' means). The cluster I referred to is the second one (medialorbitofrontal). I investigated differences in cortical area from groups 1 and 2 in contrast to groups 3 and 4 (contrast 3 as in https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V). Best, Pedro Rosa. On Mon, May 14, 2018 at 5:42 PM, Douglas N. Greve wrote: > Can you send your fsgd file and contrasts? > > > On 05/14/2018 01:25 PM, Pedro Rosa wrote: > > > > > > Dear FreeSurfers, > > I got results from a cortical area analysis that intrigued me: Upon > > the inspection of clusters that survived Monte-Carlo simulation, I > > found a cluster with larger area among a first group in contrast to a > > second group. > > However, when I calculated the cortical areas means from that cluster > > (as available in the glmdir), the second group had values slightly > > larger than the first group (i.e., showing a difference in the > > opposite direction). > > How would you explain such findings? Must I have committed a mistake > > in the analysis or its interpretation? > > Best, > > Pedro Rosa - University of São Paulo - Brazil. > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > cache.th13.abs.y.ocn2.dat Description: Binary data cache.th13.abs.sig.cluster.summary Description: Binary data C.dat Description: Binary data y.fsgd Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Contrast interpretation - between-groups mean
External Email - Use Caution Here it is: mri_glmfit-sim --glmdir PEP-HC_Gender_Age.txt.lh.area.mgh.5.mgh.cortex.glmdir --sim-sign abs --cache 1.3 abs On Mon, May 14, 2018 at 6:59 PM, Douglas N. Greve wrote: > sorry, one more thing. Can you send your mri_glmfit-sim command line? > > > On 05/14/2018 05:46 PM, Pedro Rosa wrote: > > > > > > Hi, Doug. Many thanks. > > Find the fsgd and the contrast attached, as well as the cluster > > summary and the individual-based cluster data (which I used to > > calculate the groups' means). The cluster I referred to is the second > > one (medialorbitofrontal). > > I investigated differences in cortical area from groups 1 and 2 in > > contrast to groups 3 and 4 (contrast 3 as in > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V). > > Best, > > Pedro Rosa. > > > > On Mon, May 14, 2018 at 5:42 PM, Douglas N. Greve > > mailto:dgr...@mgh.harvard.edu>> wrote: > > > > Can you send your fsgd file and contrasts? > > > > > > On 05/14/2018 01:25 PM, Pedro Rosa wrote: > > > > > > > > > Dear FreeSurfers, > > > I got results from a cortical area analysis that intrigued me: Upon > > > the inspection of clusters that survived Monte-Carlo simulation, I > > > found a cluster with larger area among a first group in contrast > > to a > > > second group. > > > However, when I calculated the cortical areas means from that > > cluster > > > (as available in the glmdir), the second group had values slightly > > > larger than the first group (i.e., showing a difference in the > > > opposite direction). > > > How would you explain such findings? Must I have committed a > > mistake > > > in the analysis or its interpretation? > > > Best, > > > Pedro Rosa - University of São Paulo - Brazil. > > > > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > The information in this e-mail is intended only for the person to > > whom it is > > addressed. If you believe this e-mail was sent to you in error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> . If the e-mail was sent > > to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Contrast interpretation - between-groups mean
External Email - Use Caution Many thanks, Doug! Should I then rely on groups' means to determine the 'direction of the result', and not on the 'max statistical significance' signal? Does 'abs' simulation sum up the results I could get by running 'pos' and 'neg' simulations separately? Best On Mon, May 14, 2018 at 7:13 PM, Douglas N. Greve wrote: > You have specified "abs" meaning an unsigned "absolute" test, so there > is no guarantee that the mean contrast will be pos or neg. > > > On 05/14/2018 06:11 PM, Pedro Rosa wrote: > > > > > > Here it is: mri_glmfit-sim --glmdir > > PEP-HC_Gender_Age.txt.lh.area.mgh.5.mgh.cortex.glmdir --sim-sign abs > > --cache 1.3 abs > > > > On Mon, May 14, 2018 at 6:59 PM, Douglas N. Greve > > mailto:dgr...@mgh.harvard.edu>> wrote: > > > > sorry, one more thing. Can you send your mri_glmfit-sim command line? > > > > > > On 05/14/2018 05:46 PM, Pedro Rosa wrote: > > > > > > > > > Hi, Doug. Many thanks. > > > Find the fsgd and the contrast attached, as well as the cluster > > > summary and the individual-based cluster data (which I used to > > > calculate the groups' means). The cluster I referred to is the > > second > > > one (medialorbitofrontal). > > > I investigated differences in cortical area from groups 1 and 2 in > > > contrast to groups 3 and 4 (contrast 3 as in > > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V > > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V>). > > > Best, > > > Pedro Rosa. > > > > > > On Mon, May 14, 2018 at 5:42 PM, Douglas N. Greve > > > mailto:dgr...@mgh.harvard.edu> > > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>> > > wrote: > > > > > > Can you send your fsgd file and contrasts? > > > > > > > > > On 05/14/2018 01:25 PM, Pedro Rosa wrote: > > > > > > > > > > > > Dear FreeSurfers, > > > > I got results from a cortical area analysis that intrigued > > me: Upon > > > > the inspection of clusters that survived Monte-Carlo > > simulation, I > > > > found a cluster with larger area among a first group in > > contrast > > > to a > > > > second group. > > > > However, when I calculated the cortical areas means from that > > > cluster > > > > (as available in the glmdir), the second group had values > > slightly > > > > larger than the first group (i.e., showing a difference in > the > > > > opposite direction). > > > > How would you explain such findings? Must I have committed a > > > mistake > > > > in the analysis or its interpretation? > > > > Best, > > > > Pedro Rosa - University of São Paulo - Brazil. > > > > > > > > > > > > ___ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >
Re: [Freesurfer] Contrast interpretation - between-groups mean
External Email - Use Caution Dear Doug, Many thanks. I ran the analysis with 'abs', 'pos' and 'neg' testing. All clusters (including the 'problematic' cluster on the medialorbitofrontal region) are present in 'abs' and 'neg' testing summaries, and not present in 'pos' testing summary. This medialorbitofrontal cluster shows a direction of effect when I consider the contrast (and the maximum statistical value signal) and the opposite direction when I analyze groups means. How should I proceed to report such result? Best, Pedro. PS: I apologize if I sent a number of empty emails to the list in the last hours. > On May 23, 2018, at 13:30, pedrogomesr...@gmail.com wrote: > > Dear Doug > > -- > Pedro > >> On May 15, 2018, at 13:36, Douglas N. Greve wrote: >> >> depends on what you are getting the direction of the result for and how >> you want to interpret it. If the cluster has both pos and neg, then the >> interpretation becomes more difficult. Is this really happening? I don't >> think I've ever seen it. The abs() just takes the absolute value, there >> is no summing across the cluster, just counting voxel above threshold. >> If you really want to evaluate the sign, you can do a signed test >> (corrections across signed and unsigned tests then become problematic). >> Finally, the 1.3 threshold is way to low when using the MC-Z simulation. >> If you want to use a threshold that low, then you'll need to use a >> permutation instead. See >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm >> >> >>> On 05/14/2018 06:33 PM, Pedro Rosa wrote: >>> >>> >>> Many thanks, Doug! >>> Should I then rely on groups' means to determine the 'direction of the >>> result', and not on the 'max statistical significance' signal? >>> Does 'abs' simulation sum up the results I could get by running 'pos' >>> and 'neg' simulations separately? >>> Best >>> >>> On Mon, May 14, 2018 at 7:13 PM, Douglas N. Greve >>> mailto:dgr...@mgh.harvard.edu>> wrote: >>> >>>You have specified "abs" meaning an unsigned "absolute" test, so >>>there >>>is no guarantee that the mean contrast will be pos or neg. >>> >>> >>>>On 05/14/2018 06:11 PM, Pedro Rosa wrote: >>>> >>>> >>>> Here it is: mri_glmfit-sim --glmdir >>>> PEP-HC_Gender_Age.txt.lh.area.mgh.5.mgh.cortex.glmdir --sim-sign >>>abs >>>> --cache 1.3 abs >>>> >>>> On Mon, May 14, 2018 at 6:59 PM, Douglas N. Greve >>>> mailto:dgr...@mgh.harvard.edu> >>><mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>> >>>wrote: >>>> >>>> sorry, one more thing. Can you send your mri_glmfit-sim >>>command line? >>>> >>>> >>>> On 05/14/2018 05:46 PM, Pedro Rosa wrote: >>>> > >>>> > >>>> > Hi, Doug. Many thanks. >>>> > Find the fsgd and the contrast attached, as well as the >>>cluster >>>> > summary and the individual-based cluster data (which I used to >>>> > calculate the groups' means). The cluster I referred to is the >>>> second >>>> > one (medialorbitofrontal). >>>> > I investigated differences in cortical area from groups 1 >>>and 2 in >>>> > contrast to groups 3 and 4 (contrast 3 as in >>>> > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V >>><https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V> >>>> <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V >>><https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V>>). >>>> > Best, >>>> > Pedro Rosa. >>>> > >>>> > On Mon, May 14, 2018 at 5:42 PM, Douglas N. Greve >>>> > mailto:dgr...@mgh.harvard.edu> >>><mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> >>>> <mailto:dgr...@mgh.harvard.edu >>><mailto:dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu >>><mailto:dgr...@mgh.harvard.edu>>>> >>>> wrote: >>>> > >>>> > Can you send your fsgd f
Re: [Freesurfer] Contrast interpretation - between-groups mean
External Email - Use Caution Hi, Doug. I am writing to ask for the Mac binaries of mri_surfcluster, as you mentioned a while ago. Can you help me? Best, Pedro. On Tue, Jun 5, 2018 at 12:09 PM, wrote: > Hi, Doug. > I manually checked for the sig values, and all I got were positive. Is > this unexpected? > > Should I write someone to get those binaries? I tried to run it again, and > was not successful. > > Many many thanks! > > -- > Pedro > > On May 29, 2018, at 12:29, Douglas Greve wrote: > > > > On 5/27/18 3:33 PM, Pedro Rosa wrote: > > > Hi, Doug. > For this specific 'problematic' cluster, the maximum statistical value > from the cluster summary is negative, that indicates a direction of result > (considering the contrast matrix I used) opposite to the one I get when I > compare means. > I inspected p-values from sig.mgh (and also p-values masked for surviving > clusters) and all seem positive. I could not actually get how inspection > sig.mgh may help to solve this issue. Can you clarify this point, please? > > I mean do you find both positive and negative values in the sig.mgh in the > vertices of the problematic cluster? I suppose it is possible, I've just > never seen it before. > > > Following your comment on the 1.3 threshold, I read the paper and the > permutation page from FreeSurfer wiki, and tried to run mri_glmfit-sim with > perm function (after mri_glmfit with -eres function) using FS6 twice, and > it seems to take many hours (~ 26 hours) to run (I am using a regular Mac > computer, not a cluster), while the wiki mentions it should take 20 > minutes. > I got this message while running it: 'INFO: design matrix is not > orthogonal, but perm forced'. Also, it ended with this error: ERROR: > Option --vwsigmax unknown., and it dit not creat the perm* files. I > attached the log, in case you want to inspect it. > > If you are on a mac, we will have to get new binaries for you. Rob, can > you get a mac version of mri_surfcluster to Pedro? > > Also, don't run mri_glmfit-sim with --bg 1 as it causes really long run > times for reasons I don't understand. If you are running with multiple > processors, then use --bg N where N is the number, but if N=1, just leave > off --bg entirely. > > Also, I changed the mri_glmfit-sim file regarding the .csh file path > ($FREESURFER_HOME/sources.csh to /SetUpFreeSurfer.csh) before running it > (it could not find sources.csh). > Many thanks, > Pedro. > > > > > On Wed, May 23, 2018 at 6:45 PM, Douglas N. Greve > wrote: > >> So the maximum is positive, but the mean is negative? When you look at >> the uncorrected p-values, can you actually find this? My guess is that >> the cluster must be largely negative, so I would report that >> >> >> On 05/23/2018 03:52 PM, Pedro Rosa wrote: >> > External Email - Use Caution >> > >> > Dear Doug, >> > Many thanks. >> > I ran the analysis with 'abs', 'pos' and 'neg' testing. >> > All clusters (including the 'problematic' cluster on the >> > medialorbitofrontal region) are present in 'abs' and 'neg' testing >> > summaries, and not present in 'pos' testing summary. >> > This medialorbitofrontal cluster shows a direction of effect when I >> > consider the contrast (and the maximum statistical value signal) and >> > the opposite direction when I analyze groups means. How should I >> > proceed to report such result? >> > Best, >> > Pedro. >> > PS: I apologize if I sent a number of empty emails to the list in the >> > last hours. >> > >> >> On May 23, 2018, at 13:30, pedrogomesr...@gmail.com wrote: >> >> >> >> Dear Doug >> >> >> >> -- >> >> Pedro >> >> >> >>> On May 15, 2018, at 13:36, Douglas N. Greve >> wrote: >> >>> >> >>> depends on what you are getting the direction of the result for and >> how >> >>> you want to interpret it. If the cluster has both pos and neg, then >> the >> >>> interpretation becomes more difficult. Is this really happening? I >> don't >> >>> think I've ever seen it. The abs() just takes the absolute value, >> there >> >>> is no summing across the cluster, just counting voxel above threshold. >> >>> If you really want to evaluate the sign, you can do a signed test >> >>> (corrections across signed and unsigned tests then become >> pr
[Freesurfer] Tracula - configuration file error
Dear all, I am facing an error at the configuration file for trac-all I am trying to run a single subject, 148, for who there is a folder ‘148’ with all DWI DICOMs and a folder ‘ESNA148’ with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is bval.bval and bvec.bvec. I attached the configuration file. However, I am facing the following error, although no run list is specified: [server:~/Desktop] pedrogomesrosa% trac-all -corr -c config.rtf Missing }. Missing }. }: Command not found. Missing }. red255green255blue255: Command not found. red240green242blue245: Command not found. }: Command not found. margl1440margr1440vieww22600viewh9020viewkind0: Command not found. deftab720: Command not found. pardpardeftab720: Command not found. ERROR: run list is longer than subject list Any input is appreciated. Regards, Pedro Rosa. config.rtf Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula - configuration file error
Hi, Thank you a lot! It now ran, but exited with errors: ERROR: fMRIframe: frame >= n frames Can you help me? Regards, Pedro Rosa [server:~/Desktop] pedrogomesrosa% trac-all -corr -c config INFO: SUBJECTS_DIR is /Users/pedrogomesrosa/Desktop INFO: Diffusion root is /Users/pedrogomesrosa/Desktop Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/Freesurfer5.3/freesurfer Previous: /Volumes/Data/Freesurfer_5.3/freesurfer trac-preproc -c /Users/pedrogomesrosa/Desktop/ESNA148/scripts/dmrirc.local -log /Users/pedrogomesrosa/Desktop/ESNA148/scripts/trac-all.log -cmd /Users/pedrogomesrosa/Desktop/ESNA148/scripts/trac-all.cmd #- /Applications/Freesurfer5.3/freesurfer/bin/trac-preproc #- #@# Image corrections Fri May 16 08:35:20 BRT 2014 mri_convert /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz mri_convert /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm... Getting Series No INFO: Found 6612 files in /Users/pedrogomesrosa/Desktop//148 INFO: Scanning for Series Number 5 Scanning Directory INFO: found 6501 files in series INFO: loading series header info. error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strings: can't open file: /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808391678947142928 (No such file or directory) error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/strings: can't open file: copy.dcm (No such file or directory) RunNo = 4 WARNING: Run 4 appears to be truncated Slice = 1, nthframe = 1, nframes = 2, 0 INFO: sorting. INFO: (120 120 1), nframes = 2, ismosaic=0 PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix - 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ERROR: nlist (6501) > nslices (1) x frames (2) ERROR: dump file list into fileinfo.txt. ERROR: check for consistency ERROR: set nlist = nslices*nframes. FileName /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808214939782717907.dcm Identification NumarisVersyngo MR B15 ScannerModel Espree PatientName RODRIGUES^ADRIANA C Date and time StudyDate 20121128 StudyTime 075625.593000 SeriesTime082207.781000 AcqTime 082147.882500 Acquisition parameters PulseSeq *ep_b0 Protocol DIF 64 2NEX 2.7mmX2mm Trigger (Ax Puro) PhEncDir COL EchoNo1 FlipAngle 90 EchoTime 110 InversionTime -1 RepetitionTime8000 PhEncFOV 240 ReadoutFOV240 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows120 NImageCols120 NFrames 2 SliceArraylSize 50 IsMosaic 0 ImgPos120.1304 78.5600 -52.6158 VolRes 2. 2. 2.7000 VolDim120 1201 Vc -1. -0. 0. Vr -0. -1. 0. Vs -0. -0. 1. VolCenter 0.1304 -41.4400 -51.2658 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=8000.00, TE=110.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz... mri_probedicom --i /Users/pedrogomesrosa/Desktop//148/1.3.12.2.1107.5.2.31.30747.2012112808371376939956.dcm > /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dcminfo.dat cp /Users/pedrogomesrosa/Desktop/bvec.bvec /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvecs cp /Users/pedrogomesrosa/Desktop/bval.bval /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvals mv -f /Users/pedrogomesrosa/Desktop/ESNA148/dmri/bvecs.tmp /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvecs mv -f /Users/pedrogomesrosa/Desktop/ESNA148/dmri/bvals.tmp /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.mghdti.bvals flip4fsl /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 10.8 fslswapdim /Users/pedrogomesrosa/Desktop/ESNA148/dmri/dwi_orig.nii.gz x -y z /Users/pedrogomesrosa/D
[Freesurfer] mri_convert frame error in tracula
Dear All, As suggest, I am reposting a previous question. I am trying to run a single subject in TRACULA (trac-all -corr -c config), 148, for who there is a folder ‘1482’ with all DWI DICOMs and a folder ‘ESNA148’ with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is bval.bval and bvec.bvec. I attached the trac-all.log that comes with the following error: ERROR: fMRIframe: frame >= frames Can anyone help me? Thank you in advance! Regards, Pedro Rosa. trac-all.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_convert frame error in tracula
Dear All, As suggested, I am reposting a previous question. I am trying to run a single subject in TRACULA (trac-all -corr -c config), 148, for who there is a folder ‘1482’ with all DWI DICOMs and a folder ‘ESNA148’ with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is bval.bval and bvec.bvec. I attached the trac-all.log that comes with the following error: ERROR: fMRIframe: frame >= frames Can anyone help me? Thank you in advance! Regards, Pedro Rosa. trac-all.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] MatLab Version and Hardware and Freesurfer Statistics
Dear list, Does the OS version, hardware or MatLab version (i.e., 2013a vs. 2014a) impacts in the results from the LME processing (Bernal-Rusiel et al.), employed after the Freesurfer 5.1/5.3 longitudinal pipeline? Regards, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula ERROR: fMRIframe: frame >= nframes
Anastasia, I was finding the same error as Jun, and your help fixed it. Thank you very much. However, I am now finding a new error (attached). Can you help me? Thank you again. Regards, Pedro Rosa. On Wednesday, July 2, 2014 at 10:49 PM, Jun Shinozaki wrote: > Hi Anastasia, > > You are right! There are empty spaces at the end of the lines in > original bvecs and bvals. > I could fix the error and finish trac-preproc without error by > eliminating these spaces. > Thank you so much! > > Regards, > Jun Shinozaki > > 2014-07-02 15:21 GMT+09:00 Anastasia Yendiki (mailto:ayend...@nmr.mgh.harvard.edu)>: > > > > There are probably some empty spaces at the end of the lines of the > > original files that confuses it into introducing those zeros. If you > > attach the original files, I can take a look at them. > > > > On Wed, 2 Jul 2014, Jun Shinozaki wrote: > > > > > Hi Anastasia, > > > > > > I created bvals.txt and bvecs.txt using dcm2nii. > > > These original files were text files and set in dmrirc profile as > > > "set bvalfile = /path/to/bvals.txt". > > > > > > I checked word count for these files > > > # wc -w bvals.txt bvecs.txt > > > 65 bvals.txt > > > 195 bvecs.txt > > > 260 total > > > > > > However, when I run "trac-all -prep -c dmrirc", then freesurfer creates > > > bvals and bvecs automatically in dmri folder. > > > > > > Then, I check word count > > > # wc -w bvals bvecs > > > 65 bvals > > > 198 bvecs > > > 263 total > > > > > > Now, freesurfer adds 3 extra entries in the bvecs file. > > > As you said, there is an extra column of zeros in the end. > > > > > > So, I cannot fix the error. > > > > > > Regards, > > > Jun Shinozaki > > > > > > 2014-07-01 15:56 GMT+09:00 Anastasia Yendiki > > > mailto:ayend...@nmr.mgh.harvard.edu)>: > > > > > > > > Hi Jun - By a simple word count on these files: > > > > > > > > % wc -w bvals bvecs > > > > 65 bvals > > > > 198 bvecs > > > > 263 total > > > > > > > > As you can see, there are 3 extra entries in the bvecs file. If you then > > > > open the file, you'll see that there is an extra column of zeros in the > > > > end. Not sure if that's what's causing the problem, but you might want > > > > to > > > > look for empty lines at the end of your original gradient table. > > > > > > > > a.y > > > > > > > > On Tue, 1 Jul 2014, Jun Shinozaki wrote: > > > > > > > > > Hi Anastasia, > > > > > Thank you for your e-mail. > > > > > I took 65 DWIs (5 b0 volumes and 60 direction DWIs). > > > > > > > > > > I checked dwi.nii.gz in the dmri folder, and dwi.nii.gz had 65 images. > > > > > Also, I checked bvals and bvecs in the dmri folder, and they have 65 > > > > > counts. > > > > > It seems consistent. > > > > > I attach bvals and bvecs. These files were created by freesurfer > > > > > automatically. > > > > > > > > > > Regards, > > > > > Jun Shinozaki > > > > > > > > > > 2014-06-30 18:38 GMT+09:00 Anastasia Yendiki > > > > > mailto:ayend...@nmr.mgh.harvard.edu)>: > > > > > > > > > > > > Hi Jun - It's failing at the point where it tries to extract the > > > > > > low-b > > > > > > images from the DWI series. I suspect that the number of frames in > > > > > > the 4D > > > > > > DWI volume that is extracted from your dicom does not match the > > > > > > number of > > > > > > frames that it expects to find based on how many gradient vectors or > > > > > > b-values it's looking for. So I'd check these DWI, gradient vector > > > > > > and > > > > > > b-value files to make sure they are all consistent. > > > > > > > > > > > > Hope this helps, > > > > > > a.y > > > > > > > > > > > > On Mon, 30 Jun 2014, Jun Shinozaki wrote: > > > > > > > > > > > > > Dear All, > > > > > > > > > > > > > > I am trying to run a sin
Re: [Freesurfer] Tracula ERROR: fMRIframe: frame >= nframes
Thank you once again! Yes, that is true. The bval and bvec file were doubled, so I removed half the values (and also the empty spaces) and the fMRIframe: frame >= nframes stopped from happening. A converted the dcm to nii using dcm2nii software, and used its bval and bvec files as input to TRACULA. Is it frequent to have a repetition of directions? I now included the doubled bvec and bval files, but it seems I have another error: [server:/MRI/Tracula-test] pedrogomesrosa% trac-all -prep -c config -no-isrunning INFO: SUBJECTS_DIR is /MRI/Tracula-test INFO: Diffusion root is /MRI/Tracula-test Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/Freesurfer5.3/freesurfer Previous: /Volumes/Data/Freesurfer_5.3/freesurfer trac-preproc -c /MRI/Tracula-test/ESNA149/scripts/dmrirc.local -log /MRI/Tracula-test/ESNA149/scripts/trac-all.log -cmd /MRI/Tracula-test/ESNA149/scripts/trac-all.cmd -no-isrunning #- /Applications/Freesurfer5.3/freesurfer/bin/trac-preproc #- #@# Image corrections Fri Jul 4 07:00:19 BRT 2014 mri_convert /MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155.dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz mri_convert /MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155.dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155.dcm... Getting Series No INFO: Found 6607 files in /MRI/Tracula-test/149 INFO: Scanning for Series Number 3 Scanning Directory INFO: found 6500 files in series INFO: loading series header info. RunNo = 2 INFO: sorting. INFO: (120 120 50), nframes = 130, ismosaic=0 PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix - 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004780512604280.dcm Identification NumarisVersyngo MR B15 ScannerModel Espree PatientName XX Date and time StudyDate 20120613 StudyTime 074845.171000 SeriesTime080047.531000 AcqTime 080046.267500 Acquisition parameters PulseSeq *ep_b0 Protocol DIF 64 2NEX 2.7mmX2mm Trigger (Ax Puro) PhEncDir COL EchoNo1 FlipAngle 90 EchoTime 110 InversionTime -1 RepetitionTime8000 PhEncFOV 240 ReadoutFOV240 Image information RunNo 2 SeriesNo 3 ImageNo 1 NImageRows120 NImageCols120 NFrames 130 SliceArraylSize 50 IsMosaic 0 ImgPos116.6747 79.4248 -34.6722 VolRes 2. 2. 2.7000 VolDim120 120 50 Vc -1. -0. 0. Vr -0. -1. -0.0052 Vs -0. -0.0052 1. VolCenter -3.3253 -40.9270 32.1985 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=8000.00, TE=110.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.86, -0.00523596) k_ras = (-0, -0.00523596, 0.86) writing to /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz... mri_probedicom --i /MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155.dcm > /MRI/Tracula-test/ESNA149/dmri/dcminfo.dat cp /MRI/Tracula-test//bvec.bvec /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvecs cp /MRI/Tracula-test//bval2.bval /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvals ERROR: Found 130 b-values but 108.333 gradient vectors Darwin server.macbookpro.com 13.2.0 Darwin Kernel Version 13.2.0: Thu Apr 17 23:03:13 PDT 2014; root:xnu-2422.100.13~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Jul 4 07:04:02 BRT 2014 Pedro Rosa On Friday, July 4, 2014 at 5:18 AM, Anastasia Yendiki wrote: > > The error message is "data and bvals/bvecs do not contain the same number > of entries". This doesn't necessarily mean that the bvecs and bvals don't > agree with each other, but that the bvecs and bvals don't agree with the > DWI data. > > Based on this line in the log file, there are 130 frames in the DWI > dicoms, so I suspect that you may have two repetitions of your 65 > directions: > > INFO: (120 120 50), nframes = 130, ismosaic=0 > > You can confirm this my looking at the images. If that is the case, you > need to have two repetitions in the bvecs/bvals files too. > > On Thu, 3 Jul 2014, Pedro Rosa wrote: > > > Hi! &
Re: [Freesurfer] Tracula ERROR: fMRIframe: frame >= nframes
Hi, Thanks a lot. I corrected the files as you suggested and now it finished without error. Best, Pedro Rosa. On Jul 4, 2014, at 7:24 AM, Anastasia Yendiki wrote: ERROR: Found 130 b-values but 108.333 gradient vectors If the b-value table has 130 entries, then the gradient table should have 130*3 entries (one x,y,z direction vector for each b-value). This error means that there are fewer entries in the gradient table than there should be. Run wc -w on these text files to check for yourself. > On Fri, 4 Jul 2014, Pedro Rosa wrote: > > Thank you once again! > Yes, that is true. > The bval and bvec file were doubled, so I removed half the values (and also > the empty spaces) and the fMRIframe: frame >= nframes stopped from > happening. > A converted the dcm to nii using dcm2nii software, and used its bval and > bvec files as input to TRACULA. Is it frequent to have a repetition of > directions? > I now included the doubled bvec and bval files, but it seems I have another > error: > [server:/MRI/Tracula-test] pedrogomesrosa% trac-all -prep -c config > -no-isrunning > INFO: SUBJECTS_DIR is /MRI/Tracula-test > INFO: Diffusion root is /MRI/Tracula-test > Actual FREESURFER_HOME /Applications/Freesurfer5.3/freesurfer > INFO: current FREESURFER_HOME does not match that of previous processing. > Current: /Applications/Freesurfer5.3/freesurfer > Previous: /Volumes/Data/Freesurfer_5.3/freesurfer > trac-preproc -c /MRI/Tracula-test/ESNA149/scripts/dmrirc.local -log > /MRI/Tracula-test/ESNA149/scripts/trac-all.log -cmd > /MRI/Tracula-test/ESNA149/scripts/trac-all.cmd -no-isrunning > #- > /Applications/Freesurfer5.3/freesurfer/bin/trac-preproc > #- > #@# Image corrections Fri Jul 4 07:00:19 BRT 2014 > mri_convert/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. > dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz > mri_convert/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. > dcm /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading > from/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. > dcm... > Getting Series No > INFO: Found 6607 files in /MRI/Tracula-test/149 > INFO: Scanning for Series Number 3 > Scanning Directory > INFO: found 6500 files in series > INFO: loading series header info. > RunNo = 2 > INFO: sorting. > INFO: (120 120 50), nframes = 130, ismosaic=0 > PE Dir COL COL > AutoAlign matrix detected > AutoAlign Matrix - > 1.000 0.000 0.000 0.000; > 0.000 1.000 0.000 0.000; > 0.000 0.000 1.000 0.000; > 0.000 0.000 0.000 1.000; > FileName/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004780512604280. > dcm > Identification > NumarisVersyngo MR B15 > ScannerModel Espree > PatientName XX > Date and time > StudyDate 20120613 > StudyTime 074845.171000 > SeriesTime080047.531000 > AcqTime 080046.267500 > Acquisition parameters > PulseSeq *ep_b0 > Protocol DIF 64 2NEX 2.7mmX2mm Trigger (Ax Puro) > PhEncDir COL > EchoNo1 > FlipAngle 90 > EchoTime 110 > InversionTime -1 > RepetitionTime8000 > PhEncFOV 240 > ReadoutFOV240 > Image information > RunNo 2 > SeriesNo 3 > ImageNo 1 > NImageRows120 > NImageCols120 > NFrames 130 > SliceArraylSize 50 > IsMosaic 0 > ImgPos116.6747 79.4248 -34.6722 > VolRes 2. 2. 2.7000 > VolDim120 120 50 > Vc -1. -0. 0. > Vr -0. -1. -0.0052 > Vs -0. -0.0052 1. > VolCenter -3.3253 -40.9270 32.1985 > TransferSyntaxUID 1.2.840.10008.1.2.1 > UseSliceScaleFactor 0 (slice 0: 1) > INFO: no Siemens slice order reversal detected (good!). > TR=8000.00, TE=110.00, TI=-1.00, flip angle=90.00 > i_ras = (-1, -0, 0) > j_ras = (-0, -0.86, -0.00523596) > k_ras = (-0, -0.00523596, 0.86) > writing to /MRI/Tracula-test/ESNA149/dmri/dwi_orig.nii.gz... > mri_probedicom > --i/MRI/Tracula-test/149/1.3.12.2.1107.5.2.31.30747.2012061308004376537404155. > dcm > /MRI/Tracula-test/ESNA149/dmri/dcminfo.dat > cp /MRI/Tracula-test//bvec.bvec > /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvecs > cp /MRI/Tracula-test//bval2.bval > /MRI/Tracula-test/ESNA149/dmri/dwi_orig.mghdti.bvals > ERROR: Found 130 b-values but 108.333 gradient ve
[Freesurfer] Uncorrected cluster information
External Email - Use Caution Dear all, I would like to obtain information regarding clusters yielded by GLM group analysis before correction for multiple comparisons (hence uncorrected). I used tksurfer to look at the clusters (sig.mgh) and was able to apply statistical thresholds, but could not obtain further information from them (as available in the .summary file after correction for multiple comparisons, such as mean cluster value, cluster size). Can you help me? Many thanks in advance, Pedro. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Using mean thickness / total area as covariates
External Email - Use Caution Dear all, I read previous threads on the list concerning the use of 'total measures' (e.g., mean thickness, total brain volune, total area) as covariates in FreeSurfer's group analysis Given that FreeSurfer analyses brain hemispheres separately, would it make more sense to use hemispheric values (i.e., lh total area in the lh area analysis and rh total area in rh area analysis) than the mean cortical value (e.g., mean between lh and rh total area in both lh and rh analyses)? Best, Pedro. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using mean thickness / total area as covariates
External Email - Use Caution Thanks, Doug! Best, Pedro. On Sun, 9 Jun 2019 at 04:31 Greve, Douglas N.,Ph.D. wrote: > This is a question about the biology. I.e., when you include mean > thickness as a covariate, you are then measuring the difference between > groups subtracting out the mean thickness of each individual. By using a > hemisphere specific value, you might introduce (or remove) > cross-hemispheric effects. > > On 6/8/2019 11:33 PM, Pedro Rosa wrote: > > External Email - Use Caution > > Dear all, > I read previous threads on the list concerning the use of 'total measures' > (e.g., mean thickness, total brain volune, total area) as covariates in > FreeSurfer's group analysis > Given that FreeSurfer analyses brain hemispheres separately, would it make > more sense to use hemispheric values (i.e., lh total area in the lh area > analysis and rh total area in rh area analysis) than the mean cortical > value (e.g., mean between lh and rh total area in both lh and rh analyses)? > Best, > Pedro. > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] LME Contrasts - Longitudinal Analysis
Dear Freesurfer List, Reading the Wiki for the GLM procedures, I understood that that covariates that are “0” in the contrast matrix are “regressed out” (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V). I would like to know if this is also true for the LME contrasts (http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels), and if this applies both for categorical (e.g., gender) and continuous variables (e.g., age in years). Thank you very much in advance, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Thin Surface
Thanks, Bruce. I pasted the mri_segment and mris_make_surfaces I found in three subjects’ logs. Expert opts would be -seg-wlo and -seg-ghi? Which values would be reasonable? Do they depend on scanning characteristics or do you have a sort of standard parameters for the software? Regards, Pedro Rosa. Subject 1: #@# WM Segmentation Mon Feb 16 09:08:56 BRST 2015 \n mri_segment brain.mgz wm.seg.mgz \n doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 105.0 +- 4.5 [80.0 --> 125.0] GM (72.0) : 70.1 +- 13.5 [30.0 --> 96.0] setting bottom of white matter range to 83.6 setting top of gray matter range to 97.1 Subject 2: WM (105.0): 105.6 +- 4.6 [80.0 --> 125.0] GM (70.0) : 68.4 +- 13.5 [30.0 --> 96.0] setting bottom of white matter range to 81.9 setting top of gray matter range to 95.4 Subject 3: WM (105.0): 105.6 +- 4.3 [80.0 --> 125.0] GM (71.0) : 69.2 +- 13.9 [30.0 --> 96.0] setting bottom of white matter range to 83.2 setting top of gray matter range to 97.1 —— Subject 1: \n mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs Subject2 lh \n only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/filled.mgz... reading volume /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/brain.finalsurfs.mgz... reading volume /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/wm.mgz... 14199 bright wm thresholded. 1723 bright non-wm voxels segmented. reading original surface position from /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/surf/lh.orig... computing class statistics... border white:347738 voxels (2.07%) border gray 336007 voxels (2.00%) WM (95.0): 96.2 +- 6.5 [70.0 --> 110.0] GM (85.0) : 81.4 +- 13.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.8 (was 70) setting MAX_BORDER_WHITE to 105.5 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 44.5 (was 40) setting MAX_GRAY to 92.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.3 (was 40) Subject 2: setting MIN_GRAY_AT_WHITE_BORDER to 70.2 (was 70) setting MAX_BORDER_WHITE to 106.6 (was 105) setting MIN_BORDER_WHITE to 84.0 (was 85) setting MAX_CSF to 56.4 (was 40) setting MAX_GRAY to 93.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.5 (was 40) Subject 3: WM (97.0): 97.9 +- 6.2 [70.0 --> 110.0] GM (87.0) : 83.8 +- 13.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 71.5 (was 70) setting MAX_BORDER_WHITE to 107.2 (was 105) setting MIN_BORDER_WHITE to 85.0 (was 85) setting MAX_CSF to 57.9 (was 40) setting MAX_GRAY to 94.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 78.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 44.4 (was 40) On Wednesday, February 18, 2015 at 7:58 PM, Bruce Fischl wrote: > can you check mri_segmet and mris_make_surfaces and see if the > auto-detected intensity parameters are reasonable? Things like max gray > at csf border and such. If not, you can set them explicitly using the > expert opts - this usually works > Bruce > On Wed, 18 Feb 2015, Pedro Rosa - Gmail > wrote: > > > Hi, > > I am resending it once I could not find it in the archives. > > Thanks, > > Pedro. > > > > Dear Freesurfers, > > I am working on a 1.5T MPRAGE sample of first-episode psychosis and > > controls, and have found that some subjects end up having thin cortical > > surfaces with frequent unsegmented deep sulci. I think this was worse with > > FreeSurfer 5.3 than with FreeSurfer 5.1. I attached some screen shots of > > aparc+aseg labeling T1.mgz from a few of these subjects. > > This seems to be a widespread cortical issue, although it was heterogeneous > > across subjects (some of them seemed to have the “caudal half" of both > > hemispheres adequately segmented), and trying to simply rerun those > > subjects was not very helpful. Should I manually work on them, rerun > > recon-all with distinct parameters, or just discard them? > > Regards, > > Pedro Rosa. > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains pati
[Freesurfer] RAM Replace
Dear all, I would like to know whether a RAM memory replacement in a Mac computer would change FreeSurfer 5.3 processing. I have a sample that was almost completely processed, but there are a few subjects whose acquisition are yet to be done. I would like know whether I could process such images after the RAM replacement without biasing the study. The change would be from a Markvision without ECC (error-correction code) to a Kingston with ECC. Thanks in advance, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Cortical Misegmentation
Dear FreeSurfer, I have found several subjects to have temporal lobe misegmentations (usually neocortical, as attached, but sometimes mesial tempporal), and less frequently in the insula. I could find in the manual editing page from the Wiki a way to fix this. How should I do it? Thanks a lot, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical Misegmentation
Hi, Bruce. Yes, it it the T1.mgz. Is it a large topological error? Can I correct it editing wm.mgz? Thanks, Pedro. On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote: > What is the background image? Is it the t1 that your reconned? Can you give > us the details about it? > > > > On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail (mailto:pedrogomesr...@gmail.com)> wrote: > > > Dear FreeSurfer, > > I have found several subjects to have temporal lobe misegmentations > > (usually neocortical, as attached, but sometimes mesial tempporal), and > > less frequently in the insula. > > I could find in the manual editing page from the Wiki a way to fix this. > > How should I do it? > > Thanks a lot, > > Pedro Rosa. > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical Misegmentation
That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel size, echo time 5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix size 256x192mm. Pedro Rosa On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl wrote: > What are your acquisition parameters, voxel size etc...? > > > > On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail (mailto:pedrogomesr...@gmail.com)> wrote: > > > Hi, Bruce. > > Yes, it it the T1.mgz. Is it a large topological error? Can I correct it > > editing wm.mgz? > > Thanks, > > Pedro. > > > > On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote: > > > > > What is the background image? Is it the t1 that your reconned? Can you > > > give us the details about it? > > > > > > > > > > > > On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail > > (mailto:pedrogomesr...@gmail.com)> wrote: > > > > > > > Dear FreeSurfer, > > > > I have found several subjects to have temporal lobe misegmentations > > > > (usually neocortical, as attached, but sometimes mesial tempporal), and > > > > less frequently in the insula. > > > > I could find in the manual editing page from the Wiki a way to fix > > > > this. How should I do it? > > > > Thanks a lot, > > > > Pedro Rosa. > > > > > > > > > > > > ___ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > The information in this e-mail is intended only for the person to whom it > > > is > > > addressed. If you believe this e-mail was sent to you in error and the > > > e-mail > > > contains patient information, please contact the Partners Compliance > > > HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > > error > > > but does not contain patient information, please contact the sender and > > > properly > > > dispose of the e-mail. > > > > > > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical Misegmentation
Hi, Bruce. I am currently putting the file (Well-C0-T1w-023-20050425_124.zip) - it will take a while. I was able to make it a lot better using the Topological Defect correction in tkmedit. Is it suitable for this task? I have not tried adding control points. This is an older data with a quite long follow-up, so unfortunately I can not change the acquisition. Sorry, I am unaware of the type of receive coil that was used. Thanks, Pedro Rosa. On Friday, March 6, 2015 at 10:28 AM, Bruce Fischl wrote: > Hi Pedro > > the instructions are at: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > > have you tried control points in the temporal wm? And what receive coil did > you use? You might be better off with something like 1.1mm isotropic if you > can change the acquisition > > cheers > Bruce > > On Fri, 6 Mar 2015, > Pedro Rosa wrote: > > > Sure. How can I do it? > > > > Sent from my iPhone > > > > On Mar 6, 2015, at 00:01, Bruce Fischl > (mailto:fis...@nmr.mgh.harvard.edu)> > > wrote: > > > > Can you put it on our ftp site instead? > > > > > > > > On Mar 5, 2015, at 9:37 PM, Pedro Rosa > (mailto:pedrogomesr...@gmail.com)> > > wrote: > > > > Hi, > > It will upload in an hour, Iguess: > > https://www.dropbox.com/sh/n9talmyxiafdt56/AADFttKFv3erLqDd48OpjQsna > > ?dl=0 > > Thanks a lot, > > Pedro. > > > > On Mar 5, 2015, at 23:32, Bruce Fischl > > mailto:fis...@nmr.mgh.harvard.edu)> wrote: > > > > Hmmm, if you upload it we will take a look > > Bruce > > > > > > > > On Mar 5, 2015, at 9:26 PM, Pedro Rosa - Gmail > > mailto:pedrogomesr...@gmail.com)> wrote: > > > > That’s from a 1.5T-SPGR GE scanner with > > 0.86x0.86x1.5mm voxel size, echo time 5.2ms, > > repetition time 21.7ms, angle 20, FOV 22, > > matrix size 256x192mm. > > > > Pedro Rosa > > > > On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl > > wrote: > > > > What are your acquisition parameters, > > voxel size etc...? > > > > > > > > On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail > > mailto:pedrogomesr...@gmail.com)> wrote: > > > > Hi, Bruce. > > Yes, it it the T1.mgz. Is it a large > > topological error? Can I correct it > > editing wm.mgz? > > Thanks, > > Pedro. > > > > On Thursday, March 5, 2015 at 10:52 PM, > > Bruce Fischl wrote: > > > > What is the background > > image? Is it the t1 that > > your reconned? Can you give > > us the details about it? > > > > > > > > On Mar 5, 2015, at 8:28 PM, Pedro > > Rosa - Gmail > > mailto:pedrogomesr...@gmail.com)> wrote: > > > > Dear FreeSurfer, > > I have found several > > subjects to have temporal > > lobe misegmentations > > (usually neocortical, as > > attached, but sometimes > > mesial tempporal), and less > > frequently in the insula. > > I could find in the manual > > editing page from the Wiki a > > way to fix this. How should > > I do it? > > Thanks a lot, > > Pedro Rosa. > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is > > intended only for the person to > > whom it is > > addressed. If you believe this > > e-mail was sent to you in error > > and the e-mail > > contains patient information, > > please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline > > . If the e-mail was sent to you in > > error > > but does not contain patient > > information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > > Freesu
[Freesurfer] Longitudinal - varying geometries
Dear FreeSurfers, I have read in the Mailing list (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32753.html and others) other users asking questioning in regard of a Warning from FreeSurfer 5.3 longitudinal pipeline (-base step): \n*** WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ***\n I am working in a sample with a longotudinal design which receives this warn, although there was no change in hardware, and (supposedly) the acquisition protocol was the same. As requested by Martin in former posts in the Mailing List, I attached the output from mri_info */rawavg.mgz. I would like to know if these differences should be considered a bias in a longitudinal study and, if they should, if there is a way to fix it. Regards, Pedro Rosa. baseline Description: Binary data fup Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal - varying geometries
Thanks, Martin. It is unfortunate to hear such news, but they are of course accurate. Hopefully this affects a small subset of subjects, and I will be able to add a covariate to it. Regards, Pedro Rosa. On Wednesday, April 1, 2015 at 12:30 PM, Martin Reuter wrote: > Hi Pedro, > > there is really no way to fix it. Especially if all you subjects changed > acquisition. If it is only a small subset, you can then include a co-variable > to account for this in your stats. You should then also test whether one > group has more of these cases than the other, or if it is distributed evenly > (in case you run a group analysis). If you are interested in analyzing other > co-variates (drug dose) you need to test if there is a correlation with > acquisition, etc. > > Reslicing will not help at all. Adding another reslicing step to only some > images will clearly bias results. > > If this change in acquisition has happened for most or all your subjects, you > can scan a subset back-to-back (with removal from scanner), with the > different protocols to see how large the effect is. The problem here is that > you need to scan a decent number to trust those results. > > Best, Martin > > > On 04/01/2015 11:21 AM, Pedro Rosa wrote: > > Hi Martin, > > Thank you for your answer. > > Is there a way to fix it? Can reslicing help? > > Or to try compenate for it in the processing or statistics? > > Regards > > > > -- > > Pedro Rosa > > > > > > On Apr 1, 2015, at 12:13, Martin Reuter > (mailto:mreu...@nmr.mgh.harvard.edu)> wrote: > > > > > Hi Pedro, > > > > > > yes, there was a bug (well, not really a bug but the check was > > > oversensitive). It was testing too many image parameters, some of them > > > could be problematic (e.g. different voxel sizes across time), and some > > > not. > > > > > > Looking at your attached files, you can see that the voxel sizes differ > > > significantly between the baseline and the follow-up > > > Baseline: > > > dimensions: 256 x 256 x 124 > > >voxel sizes: 0.8594, 0.8594, 1.5000 > > > Follow-up: > > > dimensions: 256 x 256 x 124 > > >voxel sizes: 1.0938, 1.0938, 1.5000 > > > > > > This can induce a bias. You need to keep imaging parameters fixed in a > > > longitudinal study, else you'll not know if changes are anatomical > > > changes or induced by the different imaging. > > > > > > Best, Martin > > > > > > On 04/01/2015 06:43 AM, Pedro Rosa - Gmail wrote: > > > > Dear FreeSurfers, I have read in the Mailing list > > > > (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32753.html > > > > and others) other users asking questioning in regard of a Warning from > > > > FreeSurfer 5.3 longitudinal pipeline (-base step): > > > > \n*** > > > > WARNING: Image geometries differ across time, maybe due to aquisition > > > > changes? This can potentially bias a longitudinal study! Will continue > > > > in 10s. > > > > ***\n > > > > I am working in a sample with a longotudinal design which receives > > > > this warn, although there was no change in hardware, and (supposedly) > > > > the acquisition protocol was the same. As requested by Martin in former > > > > posts in the Mailing List, I attached the output from mri_info > > > > */rawavg.mgz. I would like to know if these differences should be > > > > considered a bias in a longitudinal study and, if they should, if there > > > > is a way to fix it. Regards, Pedro Rosa. > > > > > > > > > > > > > > > > ___ Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School > > > Assistant in Neuroscience Dept. of Radiology, Massachusetts General > > > Hospital Dept. of Neurology, Massachusetts General Hospital Research > > > Affiliate Computer Science and Artificial Intelligence Lab, Dept. of > > > Electrical Engineering and Computer Science, Massachusetts Institute of > > > Technology A.A.Martinos Center for Biomedi
[Freesurfer] Insula
Dear FreeSurfers, I was correcting the topology of some subjects, and could not fix some subjects whose insula is misplaced into the temporal lobe / subcortical regions. Inspecting wm.mgz in tkmedit, it seems that there are wm voxels into the hippocampus, perhaps leading surfaces to be built there. Removing them, however, did not help (actually, it seems that it made things worse). Can you help me? I can upload the subject if it you think it is suitable. Many thanks in advance, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Insula
Hi, Thanks a lot, Bruce. These are from a 1.5T GE Signa scanner, with a T1-SPGR sequence with 0.86x0.86x1.5mm voxel size, echo time 5.2ms, resolution time 21.7ms, flip angle 20. This is an older sample we have, and I intent to replicate earlier SPM analyses but now using FreeSurfer. I acknowledge the low contrast problem, but I am having success in correcting topological errors in the temporal lobe, and only these insula problems show to be harder to deal with. Your help will be very appreciated! I am now putting the file (PedroRosa.zip) Best,, Pedro Rosa On Tuesday, April 7, 2015 at 9:29 AM, Bruce Fischl wrote: > sure, upload it and we will take a look. Can you tell us a bit about the > acquisition? It's hard to tell for sure with the parcellation overlaid, > but it looks *very* low contrast, which I'm sure is making things harder > > cheers > Bruce > On Mon, 6 Apr 2015, Pedro Rosa - Gmail > wrote: > > > Dear FreeSurfers, > > I was correcting the topology of some subjects, and could not fix some > > subjects whose insula is misplaced into the temporal lobe / subcortical > > regions. Inspecting wm.mgz in tkmedit, it seems that there are wm voxels > > into the hippocampus, perhaps leading surfaces to be built there. Removing > > them, however, did not help (actually, it seems that it made things worse). > > Can you help me? I can upload the subject if it you think it is suitable. > > Many thanks in advance, > > Pedro Rosa. > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Amazon EC2 for FreeSurfer 5.3
Dear FreeSurfer users, Has anyone succeeded in running FreeSurfer 5.3 in a cloud processing system, such as Amazon EC2? I have seen prior posts in regard of FreeSurfer 5.1 (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-November/021181.html), but not for 5.3. Regards, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Amazon EC2 for FreeSurfer 5.3
Thanks, Pedro! Pedro Rosa On Wednesday, April 29, 2015 at 7:11 PM, Pedro Paulo de Magalhães Oliveira Junior wrote: > Yes. CerebralVol.com (http://CerebralVol.com) does it > > - > Pedro Paulo de Magalhães Oliveira Junior > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br (http://www.netfilter.com.br) > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > > > On Wed, Apr 15, 2015 at 9:47 PM, Pedro Rosa - GMail (mailto:pedrogomesr...@gmail.com)> wrote: > > Dear FreeSurfer users, > > Has anyone succeeded in running FreeSurfer 5.3 in a cloud processing > > system, such as Amazon EC2? > > I have seen prior posts in regard of FreeSurfer 5.1 > > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-November/021181.html), > > but not for 5.3. > > Regards, > > Pedro Rosa. > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom it is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] dt_recon
Dear developers, I am running an analysis with dt_recon, and it seems that my DWI files are organized into three series (one larger, and two smaller, that I believe are ADC and Trace). Inputing a DICOM file to dt_recon generates a .nii file from one of the series only (the larger one, once it has many more .dcm files). Thus, it ignores the smaller series. This is the first time I am working with DWI series, so I not quite sure if this way of organizing data is usual. I would appreciate help in regard of how to deal with this data and input it into dt_recon. Regards, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] dt_recon
Thanks, Doug! Pedro Rosa On Monday, May 11, 2015 at 6:51 PM, Douglas N Greve wrote: > It sounds like you did the right thing. > > On 05/10/2015 02:41 PM, Pedro Rosa - GMail wrote: > > Dear developers, > > I am running an analysis with dt_recon, and it seems that my DWI files > > are organized into three series (one larger, and two smaller, that I > > believe are ADC and Trace). Inputing a DICOM file to dt_recon > > generates a .nii file from one of the series only (the larger one, > > once it has many more .dcm files). Thus, it ignores the smaller series. > > This is the first time I am working with DWI series, so I not quite > > sure if this way of organizing data is usual. > > I would appreciate help in regard of how to deal with this data and > > input it into dt_recon. > > Regards, > > Pedro Rosa. > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu (mailto:gr...@nmr.mgh.harvard.edu) > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > (http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html) > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] TRACULA analyses in glmfit
Dear Developers, Tracula’s Statistics wiki suggests one to use the statistical software of choice. Could it be glmfit? For that, I think I would need to concatenate each tract-by-voxel diffusion data from each subject (e.g., each diffusion data of course separately) in common space (e.g., MNI) and then input it to mri_glmfit / mri_glmfit-sim, whose output sig.mgh would be loaded in Freeview as a heatmap. I understood that diffusion data in Tracula is saved in .txt files, which cannot be inputed into mri_preproc or mri_label2vol. Is it possible to use glmfit with Tracula outputs? Thanks in advance, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA analyses in glmfit
Hi Anastasia, Thanks for the clarification. I am happy to hear that you are working on that! As the byvoxel data includes MNI coordinates, I though it could be possible to assemble them to MNI 3D space. Thanks again! Pedro Rosa. On Monday, July 6, 2015 at 12:19 PM, Anastasia Yendiki wrote: > > Hi Pedro - The point-wise stats from tracula are a 1D sequence of values, > so they cannot be analyzed with functions that work on 2D data on the > surface or 3D data in the volume. At present, you'd have to do a seperate > analysis for every point along the tract. It's on my list to implement a > more comprehensive and principled solution for this and will hopefully get > around to it soon! > > BTW, the diffusion measures are extracted by tracula in the native space, > not in a template space. An average path in template space is produced in > case you want to visualize something on an average brain, but all the > pointwise and average FA/MD/etc values are extracted in the native DWI > space of each subject. > > Best, > a.y > > On Sun, 5 Jul 2015, Pedro Rosa - GMail wrote: > > > Dear Developers, > > Tracula’s Statistics wiki suggests one to use the statistical software of > > choice. > > Could it be glmfit? > > For that, I think I would need to concatenate each tract-by-voxel diffusion > > data > > from each subject (e.g., each diffusion data of course separately) in > > common space > > (e.g., MNI) and then input it to mri_glmfit / mri_glmfit-sim, whose output > > sig.mgh > > would be loaded in Freeview as a heatmap. > > I understood that diffusion data in Tracula is saved in .txt files, which > > cannot be > > inputed into mri_preproc or mri_label2vol. Is it possible to use glmfit > > with Tracula > > outputs? > > Thanks in advance, > > Pedro Rosa. > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
