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

Re: [Freesurfer] RAM Replace

ote: > > 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 >> Free

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, 2

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: >

Re: [Freesurfer] Thin Surface

t; 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. >> >&g

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 bu

[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

Re: [Freesurfer] mris_preproc questions

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

[Freesurfer] -noskullstrip 'directive'

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 Ros

[Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

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

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

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

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 0

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

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 es

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

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

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

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

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

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: > &

Re: [Freesurfer] FWHM file not found

ope 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-

[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] glmfit and glmfit-sim after built monte-carlo simulation (superiortemporal label)

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

Re: [Freesurfer] glmfit and glmfit-sim after built monte-carlo simulation (superiortemporal label)

: > 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, > th

Re: [Freesurfer] glmfit and glmfit-sim after built monte-carlo simulation (superiortemporal label)

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

[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

[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 contin

Re: [Freesurfer] GLM - covariate question

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 gro

[Freesurfer] Local GI - longitudinal analysis

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

[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

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 &

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

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/

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

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

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' o

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, w

[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 co

[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

[Freesurfer] Contrast interpretation - between-groups mean

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

Re: [Freesurfer] Contrast interpretation - between-groups mean

l). 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? > &

Re: [Freesurfer] Contrast interpretation - between-groups mean

ine? > > > 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' me

Re: [Freesurfer] Contrast interpretation - between-groups mean

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. > > >

Re: [Freesurfer] Contrast interpretation - between-groups mean

hreshold 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,

Re: [Freesurfer] Contrast interpretation - between-groups mean

t 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, Pe

[Freesurfer] Tracula - configuration file error

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

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/pedrogomesr

[Freesurfer] mri_convert frame error in tracula

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 mail

[Freesurfer] mri_convert frame error in tracula

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 l

[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

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

Re: [Freesurfer] Tracula ERROR: fMRIframe: frame >= nframes

9/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

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

[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,

[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 i

Re: [Freesurfer] Using mean thickness / total area as covariates

btracting 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 th

[Freesurfer] LME Contrasts - Longitudinal Analysis

://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

Re: [Freesurfer] Thin Surface

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

[Freesurfer] RAM Replace

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

[Freesurfer] Cortical Misegmentation

, 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

Re: [Freesurfer] Cortical Misegmentation

gt; > > 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 temppora

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

Re: [Freesurfer] Cortical Misegmentation

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.

[Freesurfer] Longitudinal - varying geometries

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

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, > >

[Freesurfer] Insula

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

Re: [Freesurfer] Insula

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

[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

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 Oli

[Freesurfer] dt_recon

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

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

[Freesurfer] TRACULA analyses in glmfit

? 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

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