Re: [Freesurfer] visualizing paths stats by voxel

Hi Anastasia and list, sorry, I just now got around to testing out the new build of dmri_paths you sent me. Sadly, the results look about the same: Here the path stats file for the left SLFt: #!ascii label 53 1 -50.1205 2.05458 20.1324 0 2 -49.0568 1.40645 20.8743 0 3 -47.024 0.495407 22.0052

Re: [Freesurfer] Differences in the asc and FreeSurfer format of the surface data

Thanks again -- Ray Razlighi, Ph.D. Assistant Professor Quantitative Neuroimaging Laboratory Division of Cognitive Neuroscience Department of Neurology Columbia University Alt: razli...@gmail.com Office Phone: 212-342-1352 Office Fax: 212-342-1838 Website:

Re: [Freesurfer] Differences in the asc and FreeSurfer format of the surface data

Hi Ray I would assume that they are in "tkras" space, which is still "native" but is not voxel coords. cheers Bruce On Tue, 3 Nov 2015, Razlighi, Qolamreza R. wrote: Thanks Bruce, I read in another post that these coordinates in ascii file are in native space. So if I load the original

[Freesurfer] comparison of subcortical volume with 1.5 T and 3T...

Hi: I have some longitudinal study of a patient with 1.5 T images... now, we have 3T mprage images of the same patient... how can I do the comparison of the subcortical volume of the patient ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image

[Freesurfer] zcat issue, lGI processing

Hello Freesurfer Support Team, I have encountered an issue running recon-all -lgi that I believe is due to a zcat issue on mac OSx where a .Z is added to the end of the file name the resulting error looks like this... >> reading filled volume... zcat: can't stat:

[Freesurfer] subfields segmentation FS v6.0

Dear all I'm running the new pipleline for hippocampal subfields segmentation with FreeSurfer v6.0 on a T13D image. As results i can extract values for the Whole hippocampus and the following subfields: Hippocampal_tail, subiculum, CA1, hippocampal-fissure, presubiculum, parasubiculum,

Re: [Freesurfer] subfields segmentation FS v6.0

Ciao, Daniele, the alveus segmentation was very thin and unreliable, so we left it our of the results (even though it is still used in the model, and influences the fit of the atlas to the MRI scan). Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com

Re: [Freesurfer] visualizing paths stats by voxel

Dear all I'm running the new pipleline for hippocampal subfields segmentation with FreeSurfer v6.0 on a T13D image. As results i can extract values for the Whole hippocampus and the following subfields: Hippocampal_tail, subiculum, CA1, hippocampal-fissure, presubiculum, parasubiculum,

Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

Try 6.0.0beta. On 11/03/2015 12:02 PM, Clara Kühn wrote: > Our IT guy said it could be a software problem since he didn't have the > problem and the only difference between out computers was the display. > We have these versions at the institute: > > 4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0

Re: [Freesurfer] changing the index of labels

In that case you can do something like fscalc lhfile.mgz add 1000 -o lhfile1000.mgz mri_mask lhfile1000.mgz lhfile.mgz lhfile1000.mgz This will add 1000 to the lhlabels. This will make the lh labels different from the rh. You can add a constant to the rh too if you want. doug On 10/30/2015

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

Hi DOug, doug.log is attached the bash equivalent for |& is 2>&1 | thanks, Susan On Tue, 3 Nov 2015, Douglas N Greve wrote: I meant &. The & works for tcsh (or csh). Are you using bash? I'm not sure what the bash equivalent is. Maybe |2 instead of |& perhaps some bash experts can weigh in

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Dear Pablo, maybe what you want is a group x age interaction for each of those groups? (so 1x5 and 2x5)? Not sure. It is your hypothesis, your model and we usually don't give advise on model building. Since you have a special case (within family analysis) I would recommend you try to get some

Re: [Freesurfer] FreeSurfer and OpenMP

One question about "-openmp". If I run multiple "recon-all" in different terminals without using this flag... Is there any problem with the 'gcareg' stage? For example, is there any interference between subjects reconstruction? Thanks. 2015-10-16 15:07 GMT+02:00 Bruce Fischl

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

Can you run mri_glmfit-sim --debug --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space |& tee doug.log and send me doug.log? On 11/02/2015 05:08 PM, s...@u.washington.edu wrote: > Hi experts, > > I am having trouble performing a

Re: [Freesurfer] reproducing sig.mgh

Look in the output folder for a file called Xg.dat. This is the design matrix used by QDEC. Compare that to the design matrix from your ANOVA On 10/28/2015 11:13 PM, Eric Cunningham wrote: > Hello Freesurfer Experts, > > I am trying to reproduce the values in sig.mgh using matlab, just to >

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

I meant &. The & works for tcsh (or csh). Are you using bash? I'm not sure what the bash equivalent is. Maybe |2 instead of |& perhaps some bash experts can weigh in On 11/03/2015 01:41 PM, s...@u.washington.edu wrote: > Hi Doug, > > Do you mean: > >mri_glmfit-sim --debug --glmdir >

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

it cannot find this file /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm/fwhm.dat which should have been created by mri_glmfit. What is your mri_glmfit command line? Also, don't use --grf, that is for volumes only On 11/03/2015 02:27 PM,

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

Hi Doug, Do you mean: mri_glmfit-sim --debug --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2spaces |7 tee doug.log? When I tried running the same code with |& tee doug.log at the end, I kept

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

I am using bash. I am trying to google the bash equivalent of tcsh |&, but if anybody knows it, please let me know. thanks, Susan On Tue, 3 Nov 2015, Douglas N Greve wrote: > I meant &. The & works for tcsh (or csh). Are you using bash? I'm not > sure what the bash equivalent is. Maybe |2

Re: [Freesurfer] cortical thickness - comparing two groups within a ROI

The y.mgh file is created by your call to mris_preproc (or by a subsequent call to mri_surf2surf for smoothing). The order of the subjects depends on how you called mris_preproc (which should match that in the fsgd file or else everything will be bogus). The y.mgh file contains all the

Re: [Freesurfer] cortical thickness - comparing two groups within a ROI

On 10/30/2015 01:36 PM, Eryilmaz, H. Hamdi wrote: > Sorry, the figures I inserted in the text did not appear in the email. > I attach them now. > > Best, > Hamdi > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu >

Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

There was a bug in freeview in FS 5.3.0 that may have caused the crash. Clara, can you try the dev version of freeview? Ruopeng On 11/03/2015 11:50 AM, Bruce Fischl wrote: Hi Clara that doesn't crash for me. Are you sure you ahve write permission to the file? And that the disk isn't full?

Re: [Freesurfer] First-level analysis (native vs fsaverage)

In the native space analysis the data get smoothed in the 3d volume and then projecting to the surface. This is very different from a surface-based analysis where you project to the surface and then smooth in 2D. For one thing, 5mm FWHM in one analysis is not the same as 5mm FWHM in the

Re: [Freesurfer] First-level analysis (native vs fsaverage)

Thanks for your response. In general, is it better practice to run the first level analysis in the native space, and then resample the subjects to fsaverage space during concatenation, or to resample the subjects to fsaverage space during first level analysis? Best, Anais

Re: [Freesurfer] Voxel based vs surface based

I think the thing with VBM is that it is hard to get your head around what is actually being measured. The quantity is called "gray matter density" which is a number between 0 (no GM) and 1 (full GM). This is used in two overlapping contexts. At the voxel level, the density is determined by

Re: [Freesurfer] Extracing values from ces.nii

It should be interpreted as a 2D structure of size 27307*6= 163842 which are the number of vertices in fsaverage On 10/29/2015 11:41 AM, Afzal, Afsana wrote: > Hi, > > I'm trying to extract the contrast values from ces.nii.gz after > first-level analysis. My goal is to average the contrast

Re: [Freesurfer] R: Re: error vcsf.config

If there are no CSF voxels in the native functional space, there are a couple of things to do. (1) don't use a CSF regressor for any of your subjects, or (2) change the fill threshold for all subjects. The default is .95, meaning a voxel has to be at least 95% CSF for it to be classified as

Re: [Freesurfer] R: Re: average z-score of each subject from a common cluster

look in the summaryfile. Also, don't use --seg z.nii.gz. In the command below, it works because you have --annot afterwards, but in general it is not correct On 10/30/2015 04:22 PM, std...@virgilio.it wrote: > Thanks. > I have obtained: > > $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33

Re: [Freesurfer] zcat issue, lGI processing

you can find out where it is with which zcat On 11/03/2015 07:42 AM, Andrews, Derek wrote: > Hello Freesurfer Support Team, > > I have encountered an issue running recon-all –lgi that I believe is > due to a zcat issue on mac OSx where a .Z is added to the end of the > file name the

Re: [Freesurfer] First-level analysis (native vs fsaverage)

Great, thank you. In terms of smoothing, I don't want to arbitrarily increase smoothing to find effects. Is there an optimal amount of smoothing that should be performed on the surface? Thanks, Anais From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] cortical thickness - comparing two groups within a ROI

Hi Doug, Thanks for the reply. Sure I will try this command. But as it is now, how will mri_segstats know the order in the fsgd file? Also, this command needs to run for each subject, right? Then, which input file should I use for the --i flag? mri_segstats --slabel fsaverage lh

Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

Our IT guy said it could be a software problem since he didn't have the problem and the only difference between out computers was the display. We have these versions at the institute: 4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta Is the first one the dev version? Cheers,

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Dear Martin and FS experts.I have a quick query about how to obtain my design matrix of group by age from the following matlab command listed in the lme wiki. In the wiki example the matrix is created from variables 1 and 2 (group by time). X = [ones(length(M),1) M M(:,1).*M(:,2); In my case I

Re: [Freesurfer] Differences in the asc and FreeSurfer format of the surface data

It will be in an FS native coordinate system which is not interpretable by other software. What you can do is to run mris_convert with the --to-scanner option to have it save the coordinates in scanner space. If your version does not have the --to-scanner option, then get the version below

[Freesurfer] using ADNI preprocessed files in FS

Hi, Sorry for the very basic question but I have not been able to find the answer in the archives, nor anywhere else. I want to use ADNI data in FS ADNI data is available in either original DICOM or has been preprocessed in the following manner: Phillips Systems: unpreprocessed DICOM

Re: [Freesurfer] First-level analysis (native vs fsaverage)

Resample to the surface and then smooth is better. On 11/03/2015 01:12 PM, Rodriguez-Thompson, Anais wrote: > Thanks for your response. In general, is it better practice to run the first > level analysis in the native space, and then resample the subjects to > fsaverage space during

Re: [Freesurfer] First-level analysis (native vs fsaverage)

No way to know what smoothing level is optimal without actually doing the smoothing On 11/03/2015 02:22 PM, Rodriguez-Thompson, Anais wrote: > Great, thank you. In terms of smoothing, I don't want to arbitrarily increase > smoothing to find effects. Is there an optimal amount of smoothing

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

Thanks. But it is still unsuccessfully looking for "rh.cope7.mgh" in [mydata}/cope7ACroi_rh.osgm.rfx. There are a lot of .mgh files in there (ar1, beta, mask, rstd, rvar, sar1), and even more .mgh files in cope7ACroi_rh.osgm.rfx/osgm (cnr, F, gamma, gammavar, mask, and sig) but no

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed} {Disarmed}

Thank you Martin. My intention was not to enquire about advice on the statistical model but instead on how to run the matlab commad with two experimental groups. My decision is to test group by age interaction for each group. The way to proceed for this would be to create two separate matrices?

[Freesurfer] Post-Doctoral position in brain imaging – University of Geneva {Disarmed}

?Applications are invited for a Post-Doctoral position in the Brain and Language Lab (www.brainandlanguagelab.org) at the University of Geneva. The position is for 2 years (or more), and will be at the new Biotech Campus (http://www.campusbiotech.ch/en/).

[Freesurfer] Adding more than 2 covariates in QDEC

I wanted to ask if it is possible to run analysis in QDEC with more than 2 covariates for examples, instead of Age, I wanted to add depression scores or race? At the moment my qdec table has two groups, two covariates... Class Group1 Class Group2 Variables Age PainMeasure If it is not possible,

Re: [Freesurfer] Freesurfer 6.0

Hi Matt this would be a beta - the new version isn't ready to be distributed yet (although we are getting closer) Bruce On Tue, 3 Nov 2015, Hoptman, Matthew wrote: Hi all, I can see a link for Freesurfer 6.0 on the website, but when I click on it to download, it just blinks at me.  I also

[Freesurfer] Fwd: visualizing paths stats by voxel

> Begin forwarded message: > > From: Janosch Linkersdörfer > Subject: Re: visualizing paths stats by voxel > Date: 3 Nov 2015 09:37:48 CET > To: Anastasia Yendiki > Cc: freesurfer@nmr.mgh.harvard.edu > > Hi Anastasia and list, > >

Re: [Freesurfer] cortical thickness - comparing two groups within a ROI

Hi Doug, I used the following command for mris_preproc to concatenate the maps from 214 subjects: mris_preproc --f /$SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --target fsaverage --hemi lh --meas thickness --out /$SUBJECTS_DIR/Analyses_Thickness/214_PrePostFort/LH/lh_thickness_map.mgh

Re: [Freesurfer] Adding more than 2 covariates in QDEC

you will have to use the command-line stream. Check out the tutorials we have on line. You'll need to create an FSGD file (example on the wiki), then run mris_preproc, then mri_surf2surf to smooth, then mri_glmfit, then mri_glmfit-sim (to correct for multiple comparisons). doug On 11/03/2015

Re: [Freesurfer] Surface-based registration

Hi Ray the -1 means that the target is a single surface and not an atlas, but the registration is still nonlinear. The variances will all be 1 so you may have to play with the weights in the energy functional. We don't do this very much and it probably defaults to quite rigid. Try reducing

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

The correct command line is --cache 4 neg --cache-label AC On 11/03/2015 03:36 PM, s...@u.washington.edu wrote: > Hi Doug, > > > > So if I pass cope7ACroi_rh.osgm.rfx and get rid of the --grf (cannot > find any documentation about what to put instead of --grf), as in > > mri_glmfit-sim --glmdir

Re: [Freesurfer] Freesurfer 6.0

It must be an issue with your browser. Try using either of the following commands (depending on your platform) in a terminal window. Linux: wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015.tar.gz Mac OSX: curl -O

[Freesurfer] Postdoctoral Scholar in Neuroimaging of Epilepsy and Brain Tumors UCSD

Dear Freesurfers, I am writing on behalf of Dr. Carrie McDonald to advertise a Postdoctoral position with our lab at UC San Diego. Location: UCSD Multimodal Imaging Laboratory (MMIL) UCSD Center for Translational Imaging and Precision Medicine (CTIPM) Start date: Flexible, but no later

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

The fwhm.dat file was in the right place. You passed the wrong folder to mri_glmfit-sim. You should pass it cope7ACroi_rh.osgm.rfx doug On 11/03/2015 02:40 PM, s...@u.washington.edu wrote: > It's: > > mri_glmfit --y > /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh >

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

It's: mri_glmfit --y /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/lh.cope$cope.mgh --osgm --glmdir /Volumes/Data_Local/ACTWF01_ILD/PrecByLvR_ILD_xsubject/cope$cope\ACroi_lh.osgm.rfx --surf fsaverage lh --label /Applications/freesurfer/subjects/fsaverage/label/lh.AC.label fwhm.dat

Re: [Freesurfer] cortical thickness - comparing two groups within a ROI

Yes, it must be exactly the same. You can pass mris_preproc your fsgd file instead of using --f. This assures that the order will be the same On 11/03/2015 02:52 PM, Eryilmaz, H. Hamdi wrote: > Hi Doug, > > I used the following command for mris_preproc to concatenate the maps from > 214

[Freesurfer] Freesurfer 6.0

Hi all, I can see a link for Freesurfer 6.0 on the website, but when I click on it to download, it just blinks at me. I also tried to ftp to your ftp site, and unfortunately, I got the message 421 Proxy is closed (unknown user location). Could you please tell me how I could get the new version

Re: [Freesurfer] Monte Carlo in mri_glmfit-sim

When you ran mri_glmfit the first time, you had to specify a file with the --y flag. It is looking for that file now. Does that file still exist in the location where it was when you ran mri_glmfit? On 11/03/2015 04:50 PM, s...@u.washington.edu wrote: > Thanks. But it is still unsuccessfully

[Freesurfer] preproc-sess and stc question

Hi - 1) I am trying to perform preprocessing steps on functional task data that was acquired on a Phillips scanner using an interleaved acquisition. There are 42 slices and the order is

Re: [Freesurfer] unit in 'search area' in the glmfit log

Thank you Doug. I was actually referring to the following values (example of my log output below): $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Volumes/pathname cmdline mri_glmfit --y /Volumes/pathname/lh.Group_abcd.thickness.10.mgh --C

Re: [Freesurfer] unit in 'search area' in the glmfit log

On 11/03/2015 07:03 PM, Jeni Chen wrote: > Thank you Doug. I was actually referring to the following values > (example of my log output below): > > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > cwd /Volumes/pathname > cmdline mri_glmfit --y >

[Freesurfer] 1.5T vs 3.0T longitudinal study...

Hi: I have two timepoints of the same patient: the first is in 1.5T and the second in 3.0T... Is it possible to do the longitudinal study (subcortical volumes) using the Workflow Summary described in https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ?... Sincerely, Gonzalo Rojas

Re: [Freesurfer] 1.5T vs 3.0T longitudinal study...

Hi Gonzalo, it is possible to run those tools on that data. The problem is you will never know if the effect you find is due to anatomical changes or scanner / field strength differences. Maybe you could scan 10-20 controls on the 1.5 and 3 T scanner back to back , to estimate scanner

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed} {Disarmed}

Hi Pablo, setting up that matrix is designing your model. You would probably add the 2 columns (1x5 and 2x5) to your matrix. Having independent matrices for each group, is a different model (actually 2 different ones). Best, Martin On 11/03/2015 04:33 PM, pablo najt wrote: Thank you

Re: [Freesurfer] unit in 'search area' in the glmfit log

> On Nov 3, 2015, at 8:01 PM, Douglas N Greve wrote: > >> Found 9260 points in label. >> *Found 7440 voxels in mask* >> *Reshaping mriglm->mask...* >> *search space = 3795. >> >> I do see that it gives information on the number of voxels in the mask >> (which is 7440

Re: [Freesurfer] unit in 'search area' in the glmfit log

yes, mm2 On 11/3/15 9:06 PM, Chen Jen-I. wrote: >> On Nov 3, 2015, at 8:01 PM, Douglas N Greve >> wrote: >> >>> Found 9260 points in label. >>> *Found 7440 voxels in mask* >>> *Reshaping mriglm->mask...* >>> *search space = 3795. >>> >>> I do see that it gives

Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

With the FS 6 beta version the problem doesn't occur. Cheers, Clara - Ursprüngliche Mail - Von: "Ruopeng Wang" An: "Freesurfer support list" Gesendet: Dienstag, 3. November 2015 18:03:52 Betreff: Re: [Freesurfer] Freesurfer

Re: [Freesurfer] Differences in the asc and FreeSurfer format of the surface data

Thanks Bruce, I read in another post that these coordinates in ascii file are in native space. So if I load the original volume in another visualization tool (e.g. fslview), these coordinates should be right on the border of white/gray matter. Is that correct? I already checked couple of them

[Freesurfer] Freesurfer crash upon wm.mgz changes

Dear FreeSurfer experts, since last week I have the problem that FS (5.3.0) crashes when I try to save changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can always restore it by renaming the temporary file (wm.mgz~) but it obviously doen't save any changes. I've tried

Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

Hi Clara can you send us the wm.mgz and tell us exactly what you did to make it crash? thahks Bruce On Tue, 3 Nov 2015, Clara Kühn wrote: Dear FreeSurfer experts, since last week I have the problem that FS (5.3.0) crashes when I try to save changes to the wm.mgz. It closes immediately and

Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

Hi Clara that doesn't crash for me. Are you sure you ahve write permission to the file? And that the disk isn't full? Ruopeng: any other ideas? Bruce On Tue, 3 Nov 2015, Clara Kühn wrote: Hi Bruce, I attached the wm.mgz from one of my participants. It happens with any participant though.