[Freesurfer] beta weights from FS-Fast analysis

I need to extract the beta weights from a cluster identified with FS-Fast in order to compute percentage signal change. 1) I see a file called beta.nii.gz that appears to have the beta weight information. It has a four dimensional structure and the fourth dimension appears to be the beta wei

Re: [Freesurfer] mris_resample: Command not found.

Thanks for the path, Zeke. Because it didn't download as an executable file to my computer, I used "chmod +x ~/mris_resample" (FYI for others?) It looks to be running normally. Will report back when finished! Thanks again, Daniel On May 28, 2013, at 11:25 PM, wrote: > Daniel, Stefano, Oth

[Freesurfer] Fwd: Re: mris_resample: Command not found.

Daniel, Stefano, Others, A patch is now available for the "mris_resample : Command not found" error you encountered. Simply download the file from the following link and place it in your $FREESURFER_HOME/bin directory: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample

Re: [Freesurfer] Subcortical Structures not included in GM surfaces

It doesn't need fixing. Those regions aren't part of cortex and the surfaces are arbitrary there (but excluded from thickness calculations) On May 28, 2013, at 7:39 PM, Jonathan Holt wrote: > Is this normal, attached slide shows a rather common occurrence for me. Half > of the amygdala (blue

[Freesurfer] SUMA and FSFAST

I was wondering if someone could give me a summary as to how SUMA and FSFAST differ? In other words, user interface aside, what would be reasons to use one or the other? Joe Joseph Dien, Senior Research Scientis

Re: [Freesurfer] recon-all error: v5.0.0 - dataset 1

Hi! Can you please send this to me? On May 28, 2013, at 4:24 PM, Bruce Fischl wrote: > the new topo fixer will correct this problem > Bruce > On Tue, 28 May 2013, Sudhin A. Shah wrote: > >> BEST FITNESS (M) is 984.24263 >> mri =0.000 curv = 4.318 unmri = -1001.515 >> ( f=0.00

Re: [Freesurfer] hipposubfields and data

I think the resolution is important. The CA1 subfield is only about 2-2.5 mm thick after all. If this is a feature request thread now, let me add that it would be nice if the actual training algorithm was integrated into Freesurfer. There is a lot of disagreement about the most appropriate subfiel

Re: [Freesurfer] hipposubfields and data

Hi Josh, as of now, it uses nu.mgz, which is conformed and bias field corrected with N3. Koen, do you think we should add a flag to change this? The algorithm is pretty resolution-independent, and could certainly benefit from higher-res data. Cheers, /Eugenio On Tue, 2013-05-28 at 13:34 -0700, Jo

[Freesurfer] hipposubfields and data

I have read that the hippo-subfield algorithm uses the aseg for initialization, and then uses the original MRI data. By original, does that mean it up-samples the conformed 1mm data to .5mm, or does that mean it takes the original original input (i.e. my 0.7 mm isotropic MPRAGE) and upsamples it to

Re: [Freesurfer] recon-all error: v5.0.0 - dataset 2

Hi Sudhin you need to track down why this happened. First thing to look at is the tal xform Bruce On Tue, 28 May 2013, Sudhin A. Shah wrote: > > > === > *WATERSHED** > Sorting... > mri_watershed Error: > Problem in the COG calculation

Re: [Freesurfer] recon-all error: v5.0.0 - dataset 1

the new topo fixer will correct this problem Bruce On Tue, 28 May 2013, Sudhin A. Shah wrote: BEST FITNESS (M) is 984.24263 mri =0.000   curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64  ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 )   63 patches h

[Freesurfer] recon-all errors: v5.0.0; dataset 4

CORRECTING DEFECT 1 (vertices=33, convex hull=57) After retessellation of defect 1, euler #=-41 (88676,260208,171491) : difference with theory (-61) = -20 CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces v

[Freesurfer] recon-all error: v5.0.0 - dataset 3

CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64

[Freesurfer] recon-all error: v5.0.0 - dataset 2

=== *WATERSHED** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if an

[Freesurfer] recon-all error: v5.0.0 - dataset 1

BEST FITNESS (M) is 984.24263 mri =0.000 curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) 63 patches have been generated - 38 self-intersected max face = 36973(40653) - loop = 46 (73) - ntries =

Re: [Freesurfer] LME toolbox - univariate

Hi Yolanda, since you have the intercept you don't need both group1 and group2 (as one is 1 - the other), so drop beta 5 and 6 terms. If you want to test if the slope is different between the groups differ just look at beta4 which is checking if slope1-slope2 different from zero. If it is neg

Re: [Freesurfer] mri_anatomical_stats segmentation fault

yes On 05/28/2013 03:15 PM, Rob Tennyson wrote: > That explains a lot about my problem subjects. > > Just to confirm, I should use mri_label2label with fsaverage as the > source subject and the subject in question as the target? Having this > run for all of my subjects will then allow me to use

Re: [Freesurfer] mri_anatomical_stats segmentation fault

That explains a lot about my problem subjects. Just to confirm, I should use mri_label2label with fsaverage as the source subject and the subject in question as the target? Having this run for all of my subjects will then allow me to use mris_anatomical_stats for each subject. Thanks for the help

Re: [Freesurfer] mri_anatomical_stats segmentation fault

The label that you sent applies to fsaverage. If you want to use it on a different subject, you should map it to that subject with mri_label2label doug On 05/28/2013 03:00 PM, Rob Tennyson wrote: > The labels are built from areas that showed between-group functional > differences. I am able to

Re: [Freesurfer] mri_anatomical_stats segmentation fault

The labels are built from areas that showed between-group functional differences. I am able to view the label on the subject in question in freeview. Maybe I'm looking at the wrong place in the output of mris_info? Or perhaps in the wrong file. I looked at "nvertices" in our "lh.white" file. On

Re: [Freesurfer] mri_anatomical_stats segmentation fault

how did you create the label? If it has more vertices than the subject has then something is very wrong. You don't always get segfaults, you might just get garbage and never know it. doug On 05/28/2013 02:32 PM, Rob Tennyson wrote: > Hi Doug, > > It appears that the subject I'm having the PHC i

Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

what do you mean? That the vertices are not uniform? mri_segstats just computes the mean over the parcellation without reference to non-uniformity. doug On 05/28/2013 02:15 PM, Martijn Steenwijk wrote: > Sorry, indeed, my reply was too quick. Seems to work, the results are > similar to mri_anat

Re: [Freesurfer] mri_anatomical_stats segmentation fault

Hi Doug, It appears that the subject I'm having the PHC issue with has fewer than 163798 vertices - it has 123249 vertices - however, it seems that all of our subjects have fewer vertices and I do not run into an error with any other subjects with this label. Also, I'm able to load the label onto

Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

Sorry, indeed, my reply was too quick. Seems to work, the results are similar to mri_anatomical_stats. I'm not sure whether this is relevant; but the sampling seems to be not equally dense in the different regions. Does mri_segstats somehow cope with this? Best, Martijn On Tue, May 28, 2013 at 8

Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

It can do both. When you spec --annot, then it does it on the surface and you have to pass it surface data (which you already have since you ran vol2surf). doug On 05/28/2013 02:03 PM, Martijn Steenwijk wrote: > Thanks Doug for your quick reply. But mri_segstats computes the > average value in

Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

Thanks Doug for your quick reply. But mri_segstats computes the average value inside the cortical region in the volume, right? That's not wat I want to have, I want to know the average value of the data in the volume on the wm/gm surface (i sampled with projfrac = 0). Any thoughts? On Tue, May

Re: [Freesurfer] white matter volume per lobe...

You will need to create a new color table. It is currently referencing FreeSurferColorLUT.txt. If you load the segmentation as both a segmentation and the aux volume, you can see the number associated with the color. You will need to create a table similar to FreeSurferColorLUT.txt doug On 0

Re: [Freesurfer] white matter volume per lobe...

Hi Doug: It is labeled as wm-rh-fusiform and wm-lh-fusiform Sincerely, Gonzalo Rojas Costa On Tue, May 28, 2013 at 1:47 PM, Douglas N Greve wrote: > what is is labled? > > On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote: >> >> Hi Doug: >> >>I use the instructions that you told me..

Re: [Freesurfer] white matter volume per lobe...

what is is labled? On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote: > Hi Doug: > >I use the instructions that you told me... But, why I get the gray > colored region (red arrow) ?... > >Sincerely, > > > Gonzalo Rojas Costa > > >> Message: 15 >> Date: Mon, 27 May 2013 22:41:41 -0400 >> Fro

Re: [Freesurfer] mri_anatomical_stats on custom 'thickness' file

I would use mri_segstats and specify the --annot option doug On 05/28/2013 01:28 PM, Martijn Steenwijk wrote: > Dear all, > > I've created a custom '.mgh' file containing values on the cortical > surface using mri_vol2surf. I would like to compute some statistics on > this surface in the aparc

[Freesurfer] mri_anatomical_stats on custom 'thickness' file

Dear all, I've created a custom '.mgh' file containing values on the cortical surface using mri_vol2surf. I would like to compute some statistics on this surface in the aparc-areas computed by freesurfer. Can I then just use mri_anatomical_stats with option -t specifying the custom mgh file as 't

[Freesurfer] LME toolbox - univariate

Dear FreeSurfer experts, I am trying to use the LME toolbox to analyse the hippocampal change over time in a group and also among 2 groups (2 scans per subject). When I estimate the parameters with lme_fit_FS I become a warning saying that the matrix is singular and my results are NaN. I guess th

Re: [Freesurfer] mris_resample: Command not found.

Hello Daniel, This is a confirmed issue with the 64bit Mac build. A patch to fix the issue will be available shortly (~hours). I will email the list and you personally once it is available. Sorry for the inconvenience. -Zeke On 05/28/2013 11:36 AM, Barron, Daniel S wrote: > Hi Lilla, > I'm usi

Re: [Freesurfer] mris_resample: Command not found.

Hi Lilla, I'm using OSX 10.8.3 Thanks, Daniel From: Lilla Zollei [lzol...@nmr.mgh.harvard.edu] Sent: Tuesday, May 28, 2013 10:04 AM To: Barron, Daniel S Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: mris_resample: Command not found. Hi Daniel, What oper

Re: [Freesurfer] resampling surfaces to native space, mri_surf2surf not scaling properly?

The problem is with the way you are creating the registration matrix, use this instead tkregister2 --mov rawavg.mgz --targ orig.mgz --regheader --noedit --reg resamp_brain.mgz.reg doug On 05/28/2013 11:19 AM, Gunter, Geoffrey wrote: > Thanks for your response, Douglas. > > I tried your su

Re: [Freesurfer] area measurements FS5.1

We don't have an implementation of Anderson's code that we are releasing. mris_preproc (not preproc-sess) has a mechanism to perform areal interpolation that is not as good as Anderson's, but it is what we have. doug On 05/28/2013 11:19 AM, Benjamín Garzón wrote: > Thanks, Doug. > I guess it

Re: [Freesurfer] resampling surfaces to native space, mri_surf2surf not scaling properly?

Thanks for your response, Douglas. I tried your suggestion, it doesn't appear to have changed the transformation at all though. There is still no scaling being applied to the surface. Is there anything else I can try to fix this problem? Thanks, Geoff Fr

Re: [Freesurfer] area measurements FS5.1

Thanks, Doug. I guess it's the mris_preproc file there what I need, not preproc-sess... Does this version do the areal interpolation as described in Winkler 2012 'Measuring and comparing brain cortical surface area and other areal quantities

Re: [Freesurfer] mri_anatomical_stats segmentation fault

Nothing looks like it is wrong with that label. Can you verify that the white surface has not been changed since the label was created? Check how many vertices the white surface has with mris_info. The PHC label references a vertex index as high as 163798. If the white surface does not have tha

Re: [Freesurfer] mris_resample: Command not found.

Hi Daniel, What operating system are you using? Lilla On Tue, 28 May 2013, Barron, Daniel S wrote: Hello, I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3.  When I ran mri_cvs_check, my feedback was I needed to find "mri_cvs_register.settings.txt

Re: [Freesurfer] BBR Register failing

I know, but I want to see what version of bbregister you are using On 05/28/2013 10:29 AM, Salil Soman wrote: > > I did not make any changes to bbregister. > > Thank you for all your help. > > Sal > > On May 28, 2013 6:57 AM, "Douglas N Greve" > wrote: > > and

Re: [Freesurfer] command not found

Hi, I have tried : >> setenv FREESURFER_HOME /Applications/freesurfer >> source $FREESURFER_HOME/SetUpFreesurfer.csh >> tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz I got this message: dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Applications/freesurfer/bin

[Freesurfer] mris_resample: Command not found.

Hello, I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3. When I ran mri_cvs_check, my feedback was I needed to find "mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2

Re: [Freesurfer] mri_anatomical_stats segmentation fault

Rob, can you send me your label? doug On 05/27/2013 01:00 PM, Rob Tennyson wrote: > Hi All, > > I'm running "mris_anatomical_stats" with a few manually defined > labels. For a few of my subjects, I am getting the error: > "Segmentation fault" on one of the labels. However, the other manually >

Re: [Freesurfer] nuintensitycor and skullstrip problems

can you send me the whole .mgz volume? And your recon-all command line that fails? On Tue, 28 May 2013, LAOUCHEDI MAKHLOUF wrote: hi   i send you the rawavg.mgz of the subject with the massive artefact. i inform you that i proceeded differently by splitting the recon-all -all into three ste

Re: [Freesurfer] area measurements FS5.1

try that link again doug On 05/28/2013 10:16 AM, Benjamín Garzón wrote: > Hi, > > I have processed a sample with FS 5.1 and would like to do a group > analysis of surface-based area. > > According to the release notes ( ** ) there is an issue with the > conversion into standard space. I found a fo

[Freesurfer] nuintensitycor and skullstrip problems

hi   i send you the rawavg.mgz of the subject with the massive artefact. i inform you that i proceeded differently by splitting the recon-all -all into three steps (as in freesurfer wiki) : (1) recon-all -autorecon1, (2) recon-all -autorecon2 (3) recon-all -autorecon3. i just finished with the

[Freesurfer] area measurements FS5.1

Hi, I have processed a sample with FS 5.1 and would like to do a group analysis of surface-based area. According to the release notes ( ** ) there is an issue with the conversion into standard space. I found a former post pointing to a version of preproc-sess that to my understanding should fi

Re: [Freesurfer] minor bug report

This is an annoying mismatch between linux and osx. On 05/25/2013 11:09 PM, Joseph Dien wrote: > when I run: isxconcat-sess -sf sessidlist.dat -analysis CPA.sm05.lh > -all-contrasts -o secondLevel > > I get the error messages: > > secondLevel/CPA.sm05.mni305/log/isxconcat.log > > stat: illega

Re: [Freesurfer] BBR Register failing

and bbregister? On 05/28/2013 02:03 AM, Salil Soman wrote: > It was attached to my earlier email (included again here). The only > chnages I made are at lines 129 (set fsvol = brainmask) and 132 (echo > "FSVOL $fsvol"). > > -S > > > > On Mon, May 27, 2013 at 9:14 PM, Douglas Greve > mailto:gr..

Re: [Freesurfer] fix talairach transform

Hi Laouchedi these alignments look fine. I am a bit concerned at how dark your images are near the top of the head. What coil are you using? This is probably why you are having trouble. cheers Bruce On Tue, 28 May 2013, LAOUCHEDI MAKHLOUF wrote: Hi     i have a problem when running "recon-a

Re: [Freesurfer] rerun interrupted processes

Hi Valeria can you address this type of question to the list so that others can answer and learn from the answers? Yes, you can run recon-all -make all -s and it should pick up from where it left off Bruce On Tue, 28 May 2013, Valeria Contarino wrote: > Dear Bruce, > I have a new question

Re: [Freesurfer] recon-all with FLAIR error no FSL installed

If the FLAIR was acquired in the same session you might be ok, as bbregister inititialized from the headers will be close enough unless there is large-scale movement between scans. Bruce On Tue, 28 May 2013, Popescu, Veronica wrote: Dear all, How "fatal" is the FSL environment not being init