Re: [Freesurfer] Convert TAL coordinates to surface RAS coordinates

See if this helps https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 12/11/15 10:23 AM, Inês Violante wrote: > Dear experts, > > I have a set of Talairach coordinates that I want to convert to the > individual subject surf RAS coordinates. > How can I do this? > > Thank you very muc

Re: [Freesurfer] R: Re: FDR in FS-FAST

$FREESURFER_HOME/bin On 12/11/15 2:08 PM, std...@virgilio.it wrote: > Thanks, in which folder I should put this file? > > Stefano > > >> Messaggio originale >> Da: gr...@nmr.mgh.harvard.edu >> Data: 7-dic-2015 19.23 >> A: >> Ogg: Re: [Freesurfer] FDR in FS-FAST >> >> >> >> On 12/07/2015 0

Re: [Freesurfer] move annotations across hemispheres

Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg.mac On 12/18/15 10:53 AM, Peggy Skelly wrote: I downloaded the file, but cannot get it to run. I changed permissions to make it executable, but I get -bash: ./mris_apply_reg: cannot execute binary file

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

You'll see several files that begin with mgx: mgx.ctxgm.nii.gz - pvc'ed cortex gm only mgx.subctxgm.nii.gz - pvc'ed subcortical gm only mgx.gm.nii.gz - pvc'ed all gm On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote: Hello Douglas, I have run mri_gtmpvc with static PET images using the following co

Re: [Freesurfer] no aseg.stats after recon-all -all?

Does //usr/local/freesurfer5/average/lh.DKTatlas40.gcs exist? / On 12/17/15 5:53 PM, Schweren, LJS (med) wrote: Dear Freesurfer experts, I'm trying to get BrainSeg for 5 subjects. I'm running the following commands: /for scan in ... do cd $SUBJECTS_DIR recon-all -all -subjid $scan done/ It

Re: [Freesurfer] Help importing files from a previous SPM analysis

are you doing anatomical analysis (recon-all) or functional analysis (FSFAST)? On 12/20/15 8:43 PM, Luis Fernado Silva Castro de Araújo wrote: Hi all, I am just starting to learn to analyse neuroimaging data. So these are my first steps with FreeSurfer. I apologize if the question is too ba

Re: [Freesurfer] missing 3volreg.afni

what happens when you click on it? On 12/22/15 9:28 AM, Thục Trinh wrote: Hi Douglas, It still does not work. 2015-12-21 23:29 GMT+07:00 Douglas N Greve >: that link works for me. Can you try again? On 12/20/2015 02:17 AM, Thục Trinh wrote: > Hi

Re: [Freesurfer] FW: problem with hard coded directory (/scratch)

what do you mean "match the string scratch"? Can you point us to a problematic binary? On 12/22/15 11:28 AM, Fengji Geng wrote: Hi Bruce, I reported the error related to '/scratch' a couple of weeks ago. We just tested the newest version of freesurfer 6.0. It looks likes that a lot of "if (

Re: [Freesurfer] variable TR

No, you need to simultaneously estimate the T1. Mike Harms did this years ago. On 12/22/15 11:37 AM, sha...@nmr.mgh.harvard.edu wrote: > Hi Surfers > We are wondering if we can use freesurfer to analyze ECG-gated fmri. As > far as I see, mkanalysis-sess expects a fix TR. Since we are in the >

Re: [Freesurfer] missing 3volreg.afni

GMT+07:00 Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>>: what happens when you click on it? On 12/22/15 9:28 AM, Thục Trinh wrote: Hi Douglas, It still does not work. 2015-12-21 23:29 GMT+07:00 Douglas N Greve mailto:gr...@nmr.mgh.harvard.edu>>:

Re: [Freesurfer] recon-all error

It could not find any data. It is looking for something like $SUBJECTS_DIR/mine/mri/orig/001.mgz. Alternatively, you can run recon-all with -i and pass the input. On 12/22/15 10:27 PM, abdulkawi alareefi alareefi wrote: Hi Freesurfers, I am currently learning how to use freesurfer to process t

Re: [Freesurfer] recon-all issue

how different? Eg, what is the size of hippocampus in each? On 12/23/15 9:28 AM, Bruce Fischl wrote: Hi Susanne we will need the full command lines you used and screen output in order to help you cheers Bruce On Wed, 23 Dec 2015, Schell, Susanne wrote: Dear colleagues, We are recently

Re: [Freesurfer] missing 3volreg.afni

: 3dvolreg.afni Invalid null command. 2015-12-23 7:59 GMT+07:00 Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>>: Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/3dvolreg.afni On 12/22/15 7:56 PM, Thục Trinh wrote: The link is fine. But when I cli

Re: [Freesurfer] Calculating new volumes

For binarization use mri_binarize. For intersecting, you can use mri_binarize with the --mask option. If you want to add to volumes, you can use fscalc, eg fscalc vol1.mgh sum vol2.mgh -o sum.mgh fscalc has a bunch of options. Run it with -help to see On 1/11/16 11:30 AM, Julio Alberto González

Re: [Freesurfer] Visualizing GLM analysis error

also, I think that the annot_outline is a version 6 feature. On 1/14/16 1:01 PM, Bruce Fischl wrote: Hi Peter you need a colon to separate each of the modifiers you are using, not a space. So freeview -f lh.inflated:annot=aparc.annot:outline=1:overlay= cheers Bruce On Thu, 14 Jan 2016,

Re: [Freesurfer] Analyze to nii convertor

can you give us your actual command line? It should be something like mri_convert file.img file.nii On 1/20/16 11:14 PM, Mahmoudi, Fariborz wrote: Dear All, I have a set of images with analyze 75 (img/hdr) format. I want to convert them to .nii single file format. I used the following com

Re: [Freesurfer] transform statistical map in MNI to surface

On 1/22/16 6:27 AM, John Anderson wrote: Hi Bruce, I carefully followed your orientations. Kindly I still need more clarification regarding the following point: I have statistical map in MNI152 space (volume) as an output of permutation analysis using " randomise/FSL". I want to visualize thi

Re: [Freesurfer] asegstats2table for all subjects in the directory

It should take wild cards On 1/21/16 8:16 PM, Luis Fernado Silva Castro de Araújo wrote: Hi Freesurfer experts, I wonder if there is a way of extracting the stats for all patients in my last run at the same time. I have around 120 observations and the asegstats2table syntax works in such a w

Re: [Freesurfer] surf mm coordinates do not match the individual anatomy

what do you mean you have a mesh in the original subject's anatomy in nii? Where did this come from? How was it created? If not from FreeSurfer, then there is no reason to think that they coordinates would line up. FreeSurfer uses its own (somewhat esoteric) coordinate system. I would be surpr

Re: [Freesurfer] mkanalysis-sess

On 1/22/16 3:22 AM, Thục Trinh wrote: Hello, I am using mkanalysis-sess command to configure analysis and I have some questions. 1, After run preproc-sess on raw data, why would we want to repeat all the flag using for preprocessing at mkanalysis-sess (-stc up -fwhm 5). Is it gonna effect

Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

please remember to include previous correspondences. We can't remember every post ... On 1/25/16 3:39 AM, Erik Lindberg wrote: Dear Douglas and Freesufers, You suggested: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) I tried this and was expecting that I

Re: [Freesurfer] FDR map: hide very little cluster

Use the --minarea option to mri_surfcluster (not the CSD). On 1/25/16 10:39 AM, std...@virgilio.it wrote: Hi list, please, could you help me because from several days I'm trying to have a solution. I have performed a seed-based fcMRI analysis by FAST. After mri_glmfit, I have obtained a sig.nii

Re: [Freesurfer] fast_selxavg3 error when Octave is used

Is that directory in your matlab path? does it run properly in matlab? On 1/28/16 8:36 PM, m.abouelya...@gmail.com wrote: Yes, it exists in the location you mentioned… *From: *Douglas N Greve *Sent: *Friday, January 29, 2016 2:27 AM *To: *freesurfer@nmr.mgh.

Re: [Freesurfer] fast_selxavg3 error when Octave is used

yes On 1/28/16 9:31 PM, m.abouelya...@gmail.com wrote: I am running on the virtual machine where I don’t have MATLAB so I installed Octave… Maybe I should include the folder into the Octave path? *From: *Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu> *Sent: *Friday, January 29, 2

Re: [Freesurfer] Question about mri convert

you have to tell it what you want the output to be, eg, mri_convert file.dcm output.mgz On 2/3/16 4:07 AM, Edward Su wrote: Dear colleages I am trying to convert my dicom files to .mgz from Freesurfer by using the mri_convert command, but it provides me the following error: edward-virtual-mach

Re: [Freesurfer] Viewing nifti file in freeview

Can you view it in tkmedit? Are there any voxels that are super bright relative to the rest of them? One really bright voxel may cause the screen to appear black. If you click on points in the middle, are the values in the control non-zero? On 2/4/16 8:08 AM, Worker, Amanda wrote: Hi, Chan

Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values

Hi Anna, don't use --projfrac-avg as that will average the values over the ribbon (and so give non-integer results). Just use --projfrac On 2/4/16 9:07 AM, Gardumi Anna (PSYCHOLOGY) wrote: > Dear all, > > I have checked the result of projecting a map from volume to surface with > nearest neighbo

Re: [Freesurfer] unpacking error

Hi Ji Won, can you try dcmunpack? Should take the same arguments On 2/4/16 10:28 AM, Ji Won Bang wrote: Dear. Freesurfer team. Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0 and v5.3.0. The command line is: unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

I'm not sure what the difference is. Compute the mean of the 2nd column, then subtract that number from the values in the 2nd column. doug On 2/2/16 7:30 AM, Nabin Koirala wrote: Thank you for your response . Sorry but for my understanding, should i substract the mean from the data (demean) or

Re: [Freesurfer] Fw: Gray matter intensity

Hi Sabrina, sorry, I was working on a grant, and now I'm out of town until Monday. I can try to push you forward on this now, but I have to be brief. Those images where made from data created with the pctsurfcon scriopt. If you run it with --help, you will get some docs on it. This is already r

Re: [Freesurfer] unpacking error

2016-02-04 11:56 GMT-05:00 Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>>: Hi Ji Won, can you try dcmunpack? Should take the same arguments On 2/4/16 10:28 AM, Ji Won Bang wrote: Dear. Freesurfer team. Hi. Our lab tried to unpack DICOM files using

Re: [Freesurfer] seq.info

you don't need an seq.info file anymore with fsfast On 2/5/16 2:54 PM, Ji Won Bang wrote: Dear. Freesurfer team I used dcmunpack to convert DCM to nii. This command didn't generate seq.info (I couldn't find it). I'd like to create one by myself Do you know how I can c

Re: [Freesurfer] Paired analysis FSFAST

When you run isxconcat-sess add -paired-diff. This will compute 1-2 for each subject. You can then run mri_glmfit. With that FSGD file, your contrast should be 1 not 1 0 doug On 2/6/16 11:17 AM, Thục Trinh wrote: Hello, I'm working on group analysis in fMRI activation using FSFAST. I tend t

Re: [Freesurfer] FreeSurfer group analysis: mri_glmfit-sim

On 2/7/16 1:34 PM, Silas wrote: Dear FS team, I'm currently making a group analysis using the "command-line" group analysis stream in freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng

Re: [Freesurfer] To use a ROI.label as seed in FS-FAST

Use mri_label2vol to convert the label into a volume in the anatomical space and store it in $SUBJECTS_DIR/subject/mri. Make sure to use --fill-ribbon if the label is surface-based. When running fcseed-config, specify the volume with the -seg option and use -segid 1 On 2/7/16 3:16 PM, std...@v

Re: [Freesurfer] spot checking results

Even on the same operating system they will be different because there is stuff in the header that will change. Use mri_diff (volumes, segmentations, and surface overlays) or mris_diff for surfaces to check whether they are different. On 2/5/16 11:55 PM, dgw wrote: > Don, > > Running FreeSurfe

Re: [Freesurfer] tkregister2 - horizontal and coronal inverted in the functional only

On 2/5/16 12:49 PM, Ilaria Sani wrote: Dear All, I have a functional and a T1 registered, but they are not in anatomical coordinates. Do you mean neither are in the "conformed" 256^3, 1mm^3 FreeSurfer coordinates? I put the anatomical in the desired position by using tkregister2. Was the T1

Re: [Freesurfer] Volume analysis in native space vs. mni305 space

Right. FSFAST uses "three spaces": lh (surface), rh (surface), and subcortical (volume). To prevent voxels from being counted twice, we mask cortical voxels out of the volume-based analysis. On 2/5/16 11:29 AM, Rodriguez-Thompson, Anais wrote: Hi FreeSurfer experts, I'm writing to follow up

Re: [Freesurfer] Fw: Gray matter intensity

nd rh.wm.mgh > files. What should be the next step for creating those maps? Unsure on how to > overlay the mgh files. > > Thanks, > Sabrina >> On Feb 4, 2016, at 4:48 PM, Douglas Greve wrote: >> >> Hi Sabrina, sorry, I was working on a grant, and now I'm

Re: [Freesurfer] generate .mgz file from DICOM

It looks like there is a lot of information missing from the dicom file. Did it come directly from the scanner? Or was it transformed in some way? Anonymized? On 2/4/16 5:06 PM, Kan Ding wrote: Hi, I am having trouble to generate .mgz file from DICOM. However, I was able to run the same co

Re: [Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN

Can you send me the Xtmp.mat file? On 2/2/16 6:40 PM, Mcnorgan, Christopher wrote: > Hi, > I'm attempting an inaugural run through the FS pipeline on some event-related > data collected over 6 runs. I'm not sure if this makes any difference, but > the experiment is self-paced, and the events a

Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values

There is not a single command to do this, but there is a bit of a hack that will work assuming the value you don't want to include is 0. You will have to run mri_vol2surf multiple times using a different projection fraction, creating a different file for each. Then use mri_concat to concatenat

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

. Could it be something else ? Thank you. Regards, Nabin On Thu, Feb 4, 2016 at 5:59 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: I'm not sure what the difference is. Compute the mean of the 2nd column, then subtract that number from the values in the 2nd colum

Re: [Freesurfer] Zero angle for retinotopy

Yes, 0 is where the wedge starts. doug On 2/7/16 7:56 AM, Mohamed Abdelhack wrote: Does this mean that the zero angle is the one where the wedge starts rotating in the experiment? Does this apply to eccentricity experiment also (In my lab's protocol it doesn't start from zero)? On Sat, Feb 6

Re: [Freesurfer] error in motion correction

In 4.5 I don't think there is a way to run it when different runs have different number of slices. Version 5+ will handle it properly. If you really want to use 4.5, then you'll have to put it in a different functional subdir (FSD, eg, bold), and create a new analysis for it, then combine them

Re: [Freesurfer] To use a ROI.label as seed in FS-FAST

sess.55700/avgwf.mgh Segmentation fault Messaggio originale Da: Douglas Greve Data: 8-feb-2016 4.38 A: Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST Use mri_label2vol to convert the label into a

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

files and one phase difference file). Do I just divide the values by two with something like fslmaths since it seems to have exactly double the required range? Joe On Nov 26, 2014, at 21:36, Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>> wrote: It is there again. I don't

Re: [Freesurfer] Permission denied error with mri_surfcluster command

There is a (very long) command line on that page. Mainly you need a csd file. To get that you need the FWHM of your analysis, the voxel-wise threshold, and the sign of the contrast (or abs). Then the relevant output will be the --sum. You can run it with --help to get more info. On 2/10/16 5:1

Re: [Freesurfer] comparison between two hemisphere in single

What is your mris_preproc command line? If you run mris_preproc with --xhemi, it should give you two frames (left hemi and right hemi). If you want to compute left-right, then add --paired-diff to the command line. The output will be on the lh of fsaverage_sym. This can be displayed on the whit

Re: [Freesurfer] Paired t-test for correlation analysis on two time points

I think so. Just make sure you don't try to draw conclusions from the ROI or area around it. On 2/19/16 2:02 AM, amirhossein manzouri wrote: Yes, I extracted the mean thickness of the ROI label from each timepoint to use it as a continuous variable and study the correlation of whole brain thic

Re: [Freesurfer] Paired t-test for correlation analysis on two time points

then select the ROI as continuous and group as discreet with DODS, right? Best regards, Amirhossein Manzouri On Fri, Feb 19, 2016 at 4:28 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: I think so. Just make sure you don't try to draw conclusions from the

Re: [Freesurfer] Use of gcs altlas with freesurfer on T1 image

On 2/19/16 11:00 AM, Thomas Jacquemont wrote: > Dear FreeSurfer experts, > > I would like to use the P. Hagmann atlas (Lausanne 2008 available here > https://github.com/LTS5/cmp/tree/master/cmp/data/colortable_and_gcs) on my > subjects. I ran Recon all on their T1 images and then these two comman

Re: [Freesurfer] bbregister problems

If you have spm, you can use --init-spm. Alternatively, you can use mri_coreg instead of bbr (bbr is not as effective on blurry data) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg mri_coreg --s $fs --mov ${pet_ext}_LIA.nii --lta output.lta Also, why is the top of the

Re: [Freesurfer] Corrupted head surface with mkheadsurf?

Can you load it in tksurfer or freeview? On 2/23/16 8:58 AM, Maheen Siddiqui wrote: Hi FreeSurfer users, I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not o

Re: [Freesurfer] Corrupted head surface with mkheadsurf?

!! On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: Can you load it in tksurfer or freeview? On 2/23/16 8:58 AM, Maheen Siddiqui wrote: Hi FreeSurfer users, I have used the "mkheadsurf" command to create a head su

Re: [Freesurfer] Still age corrected?

Where are you getting the mean value for each subject? Only the gamma.mgh file will be corrected. On 2/23/16 7:43 AM, Daniel Baena Pérez wrote: Dear Freesurfer user, We have performed group contrasts on cortical thickness correcting by age. Now we want to use the mean cortical thickness of on

Re: [Freesurfer] Convert spm volume to fresurfer surface

It depends on the space you used for your SPM analysis. If you used the mni152, then you should run recon-all on that, the use mri_vol2surf with --regheader, probably specifying --projfrac-max 0 1 .1 Then use mri_surf2surf to map it to fsaverage space, then use mri_binarize to binarize it at t

Re: [Freesurfer] FreeSurfer group analysis: mri_glmfit-sim

lysis/S1M1/fsaverage/rh/*cortex*/ ? Best, Silas *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve *Sent:* Monday, February 8, 2016 4:35 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [

Re: [Freesurfer] Corrupted head surface with mkheadsurf?

corrupted? If you can view it in tksurfer/freeview, then it is probably not corrupted. I vaguely remember that there was some problem reading this file in matlab, but I don't remember every coming up with a fix On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve mailto:gr...@nmr.mgh.harvar

Re: [Freesurfer] mris_anatomical_stats -th3

Without -th3, it will compute cortical volume using thickness*surface area. With -th3 it computes volume using truncated tetrahedra. -th3 will become the default in v6 (requiring -no-th3 to revert back to thickness*area) On 3/14/16 10:49 AM, Kaiming Yin wrote: Dear Douglas, I saw the previou

Re: [Freesurfer] group analysis all measures same results

Check whether rh.ad_hv.thick.10.mgh and rh.ad_hv.area.10.mgh are the same, ie, mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh If those are the same, then check whether thickness.fwhm10.fsaverage and area.fwhm10.fsaverage are the same in each subject On 3/14/16 10:53 AM, Kaiming Yin wr

Re: [Freesurfer] group analysis all measures same results

0.mgh rh.ad_hv.area.10.mgh diffcount 0 mri_diff rh.thickness.fwhm10.fsaverage.mgh rh.area.fwhm10.fsaverage.mgh diffcount 0 Does this mean I run the "-qcache" wrongly? I just run "recon-all -s XX -qcache" on each subject. Thanks, Kaiming On 14 March 2016 at 14:58,

Re: [Freesurfer] tksurfer

? Bests, John *Sent:* Wednesday, March 16, 2016 at 10:42 AM *From:* "Douglas Greve" *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] tksurfer it looks like the cluster is covering most of the brain, including precentral gyrus. The precentral gyrus ROI in the table file indic

Re: [Freesurfer] gnumeric file

On 3/16/16 6:52 AM, Caroline Beelen wrote: Hi FS team, Sorry for these rather basic questions… I'm not sure whether the gnumeric file is an ascii file (see mails below). Attached you'll find the file. It seems the case when you open it in the terminal screen that the nr's look fine (with c

Re: [Freesurfer] cannot allocate memory

that's going to create a pretty big volume as it will map your functional time course to a 256^3 float volume. If you have 100 time points, then that will be about 7G. On 3/16/16 3:27 PM, Ehsan Tadayon wrote: Hi Bruce, Thanks for your response. I'm using : freesurfer version: freesurfer-Darw

Re: [Freesurfer] AAL 3D rendering with subcorticals

Did you check the volume to verify that at least one voxel has an index = 75 ? On 3/19/16 10:43 AM, João V. Dornas wrote: Dear friends, I am following this procedures to plot a 3D rendering of the AAL volume (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27707.html). My

Re: [Freesurfer] tksurfer

it looks like the cluster is covering most of the brain, including precentral gyrus. The precentral gyrus ROI in the table file indicates that is where the peak of the cluster is and does not mean that the cluster is confined to that ROI On 3/16/16 9:43 AM, John Anderson wrote: Dear experts,

Re: [Freesurfer] error while running dt-recon all

Can you send me what dt_recon prints to the screen when your run the command below? On 3/15/16 11:40 PM, Jasmin Alves wrote: Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40 INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/

Re: [Freesurfer] aparc stats volume outputting area instead

There is not actually a "-meas" option. It should be either " -m volume" or " --measure=volume". Strange, it should have exited with an error but some reason it did not and used area as the default. On 3/16/16 10:27 AM, Clare Loane wrote: Hi Doug, I am using version 5.3 and the terminal out

Re: [Freesurfer] extracting pial surface area numbers...

That number is the mean vertex area, so to get the total area for each subject multiply that number by the number of vertices in the cluster. On 3/21/16 2:29 PM, Karl Liu wrote: Dear FS team, My question is how I should extract the measure of pial surface area from a significant cluster aft

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

>> >> Can you please upload the updated version of epidewarp.fsl for FSL 5.x. >> >> Thanks a lot, Amelia >> >> *From:*freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas >> Greve &

Re: [Freesurfer] Create a surface overlay with statistic results using AAL ROI

There is not an easy way to do this. You'd have to make an annotation from the AAL. Possible, but not easy. On 3/21/16 3:54 PM, carolina.mr wrote: Hi all, I have some statistical results for AAL 90 coordinates (correlation coefficients from network measurements x clinical data). I would like t

Re: [Freesurfer] Troubleshooting for error - neither NIfTI-1 qform or sform are valid

To check whether the orientation is correct, you can view it in freeview or tkmedit. When you click on the axial view it should show up axially, etc. Though you cannot tell whether it is left-right reversed this way. You cannot feed it a matrix, but you can specify the direction cosines on the

Re: [Freesurfer] Troubleshooting for error - neither NIfTI-1 qform or sform are valid

nical Neuropsychology Health Resources and Services Administration (HRSA) Fellow Department of Psychology Georgia State University Email: rjayak...@student.gsu.edu <mailto:rjayak...@student.gsu.edu> Message: 24 Date: Tue, 22 Mar 2016 10:56:40 -0400 From: Douglas Grev

Re: [Freesurfer] PET voxelwise

On 3/23/16 9:07 AM, Elijah Mak wrote: mri_concat --f pib_lh_fsaverage (textfile of subjects and their images) --o concat_lh_pet.mgh Should I add -mean here for the GLM? No, that is handled by glmfit mri_glmfit --y concat_lh_pet.mgh --fsgd pib_fsgd --C group1.group2.mtx --surf fsaver

Re: [Freesurfer] PET voxelwise

No, you'll need to pass the new registration to mri_vol2surf. You should also check that freeview is producing the correct registration file. We've had several problems with it that are definitely fixed in 6.0, but not sure about 5.3. Try loading it in tkregister (--lta your.lta --reg your.reg

Re: [Freesurfer] Nonisotropic PSF in mri_gtmpvc

yes, you can use --psf-col, --psf-row, and --psf-slice. --psf-col is the FWHM in the left-right direction (when the images are axial), --psf-row for the anterior-posterior, and --psf-slice is in the z-direction On 4/6/16 12:39 PM, Ian Kennedy wrote: Hello, Is there a way to specify a nonisotr

Re: [Freesurfer] bbregister --init-spm with Freesurfer 6.0

Is $FREESURFER_HOME/matlab in your matlab path? Also, I wrote a new program called mri_coreg that replicates the functionality of spmregister. This is now the default (no need to spec an init method), and I encourage you to use it. On 4/6/16 12:03 AM, Ajay Kurani wrote: Hi Freesurfer Experts,

Re: [Freesurfer] mri_vol2surf after recon-all

For the 152, you can run mni152reg --s subject, then specify $SUBJECTS_DIR/subject/mri/transform/mni152reg.dat (or .lta) for the argument to --reg. I'll need to figure out how to generate a .dat/.lta for the 305. On 4/6/16 12:50 PM, Trisanna Sprung-Much wrote: Any ideas? Trisanna -- Ph.D.

Re: [Freesurfer] bbregister --init-spm with Freesurfer 6.0

--epi-mask is a simple flag without any options. It tells bbregsiter to exclude certain regions from the surface-based parcellation (?h.aparc.annot). The regions can be gleened from the code below B0Annots[0] = CTABentryNameToAnnotation("middletemporal",lhwm->ct); B0Annots[1] = CTA

Re: [Freesurfer] rcbf-merge

sorry, this software is no longer being supported. On 4/6/16 2:37 PM, Alshikho, Mohamad J. wrote: Dear Experts, I am working on ASL analysis using Freesurfer’s tools “rcbf-prep” and “rcbf-merge” I can’t find the script “rcbf-merge” in Freesurfer 5.3 ( i.e when I call the command rcbf-merge

Re: [Freesurfer] octave fast_selxavg3() failed\n

you don't have permissions to that folder. You need to be superuser and then give yourself execution and read permission. On 4/5/16 5:22 PM, std...@virgilio.it wrote: Hi list this error occurs using octave in FS-FAST. Thanks, Stefano --- octave output LD_LIBRARY_PATH

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, then I ran my own Monte-Carlo simulation

Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

In most neuroimaging, people use p<.01 (sig threshold > 2). It is more important to have a more stringent threshold when using gaussian random fields because the assumptions built into it. Since we use simulations directly, we don't have problems with those assumptions and so I think you can go

Re: [Freesurfer] correcting mri_glmfit results

Looks like you are analyzing a table of data (ie, ROI analysis). In this case you cannot use clusterwise correction because you cannot form clusters of voxels when you don't have a voxel-wise analysis! You can do a bonferroni or FDR correction. You can get an FDR program from here ftp://surfer

Re: [Freesurfer] identity.nofile

Can you load another label, eg, lh.cortex.label? Also, I noticed that there is a space between "label=" and "/data/..." in the command line below. That space should not be there, so if it was there when you ran the command try again without the space. On 4/19/16 9:19 PM, Trisanna Sprung-Much w

Re: [Freesurfer] lh-WhiteSurfArea

It is in subject/stats/lh.aparc.stats what do you mean show it on a surface? It is just the surface area in mm^2 of the white surface On 4/23/16 11:02 AM, Hassan bakhshi wrote: Hello, In Freesurfer stats there is a feature named lh-WhiteSurfArea. where is exactly this WhiteSurfArea and how c

Re: [Freesurfer] coordinates to values

I don't think there is a command to do this. I'd probably do it in matlab. Info about the coordinates can be found here https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems Each mgz volume has a voxel-to-RAS matrix, if you invert that, and multiply your RAS you will get the column, row,

Re: [Freesurfer] registration of intraparietal sulcus

I don't have anything to do this. On 4/30/16 10:26 AM, Bruce Fischl wrote: > not that I know of, but Doug might have something. I would do it in matlab > I guess > > On Sat, 30 Apr 2016, Bastian Cheng wrote: > >> Hi Bruce! >> >> sounds good, thank you! >> >> is there a specific command to do that?

Re: [Freesurfer] no recon button

freeview does not have a recon button. You have to run recon-all from the command line. On 5/2/16 12:14 PM, Burke,Sarah E wrote: Hello, I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for

Re: [Freesurfer] no recon button

he tutorial data set before you begin. If you choose not to ... *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve *Sent:* Monday, May 2, 2016 1:29 PM *To:* freesurfer@nmr.mgh.harvard.edu *Su

Re: [Freesurfer] Freesurfer 6.0 -qcache vs mris_fwhm

Underneath, they both use the same code, so they should give the same results. Are you saying they are different? I don't know what SurfFWHM is doing so I can't comment on what those results mean. Measuring the FWHM on the surface is quite tricky. doug On 5/4/16 6:41 PM, Ajay Kurani wrote: H

Re: [Freesurfer] Extracting BOLD from a flattened surface

So you have 1 column, but you want 1 column for each vertex? We don't have anything to do that, but you can do it in matlab, eg, M = fast_vol2mat(MRIread('lh.yourdata.mgh')); M will be a 240x127000 matrix On 5/4/16 8:36 PM, Taha Abdullah wrote: Hello Doug, Sorry for the confusing and long emai

Re: [Freesurfer] Stats for Yeo and Choi Parcellations

On 5/4/16 11:40 PM, Bronwyn Overs wrote: Hi Freesurfer Mailing List, I wish to extract stats for my sample for the Yeo 2011 cortical parcellations and the Choi 2012 striatal parcellations (7 networks) that are provided for download on the freesurfer wiki. My questions are as follows: 1. I

Re: [Freesurfer] mri_glmfit-sim error

how did you compute the difference? Can you send the mris_preproc and mri_surf2surf command lines? On 5/9/16 10:26 PM, Govindarajan, Koushik Athreya wrote: > First did the mris_preproc and then the mri_surf2surf. Followed the group > analysis wiki basically. > > Thanks > Koushik > >

Re: [Freesurfer] cerebellar surface

The cerebellar surface is not going to be very accurate. You need very high resolution to model the cerebellelar surface. On 5/10/16 9:37 PM, Thomas Yeo wrote: Hi Jim, Yes. I believe so. Regards, Thomas On Tue, May 10, 2016 at 9:32 PM, Alexopoulos, Dimitrios mailto:alexopoulo...@kids.wustl.

Re: [Freesurfer] group roi to individual native functional

Register your average subject to each individual with mri_coreg (see below) using --s subject --dof 12, then use mri_label2vol with --seg ROI.nii.gz to map the ROI into the individual space. If the ROI is surface-based, then you could recon-all your average, map the ROI to the surface with mri

Re: [Freesurfer] QDEC - cannot allocate memory

OK, it is failing on the mri_concat command. It may be that one of those inputs is causing the problem. Can you run the command with each input separately, eg, mri_concat /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-1.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh --o deleteme.mg

Re: [Freesurfer] R: Re: mri_surf2vol

by default it is sphere.reg. For this there is no reason to change it. On 5/13/16 7:05 PM, std...@virgilio.it wrote: > Thanks. > I'm reading the surf2surf help but I do not understand the --trgsurfreg > options. > I'using > mri_surf2surf --hemi rh --srcsubject fsaverage --srcsurfval thickness -- >

Re: [Freesurfer] visualization tk surfer

Yes, if you set the clusterwise threshold to 0.05, you will only see clusters that or more significant. On 5/14/16 2:13 PM, maaike rive wrote: Dear Freesurfer experts, I have a question regarding tk surfer. If I load the cache.h13.abs.sig.cluster.mgh file, I'll only see the clusters survivin

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