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30099 discussions

rawfunc2surf-sess with a limited set of surface files
by Reza Rajimehr 05 Oct '14

05 Oct '14

Hi, I want to use rawfunc2surf-sess to project the functional data onto the surface in the source subject and then in the target subject. My source subject has been processed in Freesurfer. However, my target subject has been processed in Caret, so I do not have all the surface files for the target subject. To get rawfunc2surf-sess to work for my situation, I have to make some minor changes in its code. By looking at the code, I realized that rawfunc2surf-sess calls mri_vol2surf for mask and raw data, then it calls mris_fwhm to smooth raw data within mask. I am describing the changes that I have to make in these two commands, plus a specific question for each change: 1) mri_vol2surf includes the --cortex flag. Since I do not have cortex.label in the target subject, I am removing this flag. Would this be problematic later on? I will eventually do specific analyses on the occipito-temporal vertices in Matlab. Since I have lobar labels in the target subject, I can select/mask those vertices later on. 2) For the source subject, I have the white and pial surfaces. For the target subject, I have the midthickness surface which is somewhere between white and pial. I am adding --surf midthickness in mri_vol2surf to specify the target surface to be midthickness (instead of white). Will this be a problem when the source subject does not have such surface? 3) There is --projfrac 0.5 in mri_vol2surf. The help says "When [the projfrac is] set at 0.5 with the white surface, this should sample in the middle of the cortical surface. This requires that a ?h.thickness file exist for the source subject". I have the thickness file in the source subject - though I don't have it in the target subject. Does 'projfracing' happen only for the source subject? 4) I assume that mris_fwhm will work fine for my situation, unless it requires the white surface in the target subject. Which file is used in mris_fwhm for extracting the vertices coordinates? Thanks in advance for your advice, Reza

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Re: [Freesurfer] Freesurfer Digest, Vol 127, Issue 37
by Nikita Zhitkevich 04 Oct '14

04 Oct '14

Hi Bruce, I'm running Ubuntu version 14.04 LTS and Freesurfer version 1.379.2.65. I am only trying to run the Bert test lines when I come up with the segfault error I mentioned earlier so command line : tkmedit bert orig.mgz which comes up with ERROR: A segfault has occurred. This is not your fault, but is most likely an unrecoverable error and has made the program unstable. Please send the contents of the file .xdebug_tkmedit that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu. which is the only message displayed at that point. Any suggestions? Nikita Zhitkevich > From: freesurfer-request(a)nmr.mgh.harvard.edu > Subject: Freesurfer Digest, Vol 127, Issue 37 > To: freesurfer(a)nmr.mgh.harvard.edu > Date: Wed, 24 Sep 2014 12:00:02 -0400 > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. longitudinal analysis and linear mixed effects models > (Emma Thompson) > 2. Re: Pial Surface Incorrect For Native T1 (Zachary Greenberg) > 3. Segfault Error (Nikita Zhitkevich) > 4. how to extract the individual cortical thickness or volume > value of significant cluster after RFT correction (wang kangcheng) > 5. Re: how to extract the individual cortical thickness or > volume value of significant cluster after RFT correction > (wang kangcheng) > 6. Re: Segfault Error (Bruce Fischl) > 7. Re: longitudinal analysis and linear mixed effects models > (Martin Reuter) > 8. Re: Vertex wise analysis and area/pial area/volume > interpretation (Las Blawimo) > 9. Brainhack Eastern Standard Time - Boston October 18-19, 2014 > (MCLAREN, Donald) > 10. watershed problem (Anastasia Klimovich-Smith) > 11. Re: how to extract the individual cortical thickness or > volume value of significant cluster after RFT correction > (Douglas N Greve) > 12. Re: Pial Surface Incorrect For Native T1 (Douglas N Greve) > 13. Re: Scatter plot from mri_glmfit analyses (Douglas N Greve) > 14. Re: possible to use freesurfer segmentations to get mean > values for anatomic structures from other sequences (Douglas N Greve) > 15. Re: Volume to surface coordinates (Douglas N Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 23 Sep 2014 17:55:27 -0400 > From: Emma Thompson <voneconomos(a)gmail.com> > Subject: [Freesurfer] longitudinal analysis and linear mixed effects > models > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CA+BXJQJHWhSi2p+Yr25Cb_yUxcb-hEwPwCbdtV96Y=ub+Qh_8A(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi FS, > I want to conduct a within-subjects longitudinal analysis, I thought I > would be able to run a LME model in QDEC but this doesn't seem to be the > case at all, is this correct? It seems I have to do everything using Matlab > (big sigh). > > https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels > > > I have already preprocessed the data: 1) cross for all time points, 2) > base, and then 3) long according to the awesome tutorial provided by FS. > > I have only one group, a patient population that was scanned prior to > (bseline) and at various time points (3 time points post) following > treatment. Would you agree that the best analytical approach for me would > be the LME model, especially since I have a few subjects with a couple of > missing post-treatment time points? > > Is there any way you would recommend another approach using QDEC? > > Lastly, I have done everything in FS version 5.1, I'm considering upgrading > to 5.3, since my freeview software seems to be out of date. It also seems > that the Matlab tools I need to run LME are only available in FS version > 5.2. At this point a little concerned since I'm hoping I didn't waste a > bunch of time just realizing all this now, would upgrading to 5.3 > negatively impact all the work I've done thus far using version 5.1? > > Thanks for the help!! >

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Re: [Freesurfer] A question about spherical registration
by Reza Rajimehr 04 Oct '14

04 Oct '14

Hi Doug, Before I saw your response, I modified make_average_surface code by removing -annot aparc flag in the mris_make_template command within this code, and my script worked fine all the way to the end without any error. The change you made in make_average_surface would be useful in future. Just a minor point: You have modified this part: set cmd = (mris_make_template -norot aparc \ $hemi $sphere_reg $SUBJECTS $atlas) if($UseAnnot) set cmd = ($cmd -annot) Not sure if aparc should be kept in the line ... Best, Reza It is trying to use the annotation when making the registration tif. This is hard coded in your version of make_average_surface. I've attached a new version. Run it with --no-annot. Let me know if it works and I'll check it into our distribution doug

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R: Re: mri_binarize error
by stdp82＠virgilio.it 03 Oct '14

03 Oct '14

My apologies the error is in the pathway. I did not add /mri to /Applications/freesurfer/subjects/Control20 Regards, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 3-ott-2014 22.03 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] mri_binarize error does that file exist and do you have read permissions? On 10/03/2014 04:02 PM, stdp82(a)virgilio.it wrote: > Hi list > > I'm running > > mri_binarize --i aparc+aseg.mgz --match 1005 1008 1010 1025 1029 1031 > --o lh.parietal.nii.gz > > and I get this error: > > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ > cwd /Applications/freesurfer/subjects/Control20 > cmdline mri_binarize --i aparc+aseg.mgz --match 1005 1008 1010 1025 > 1029 1031 --o lh.parietal.nii.gz > sysname Darwin > hostname iMac-di-Stefano.local > machine x86_64 > user Stefano > > input aparc+aseg.mgz > frame 0 > nErode3d 0 > nErode2d 0 > output lh.parietal.nii.gz > Binarizing based on matching values > nMatch 6 > 0 1005 > 1 1008 > 2 1010 > 3 1025 > 4 1029 > 5 1031 > binval 1 > binvalnot 0 > mghRead(/Applications/freesurfer/subjects//Control20/aparc+aseg.mgz, > -1): could not open file > > Thanks > > Regards, > > Stefano > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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mri_binarize error
by stdp82＠virgilio.it 03 Oct '14

03 Oct '14

Hi list I'm running mri_binarize --i aparc+aseg.mgz --match 1005 1008 1010 1025 1029 1031 --o lh.parietal.nii.gz and I get this error: $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $cwd /Applications/freesurfer/subjects/Control20cmdline mri_binarize --i aparc+aseg.mgz --match 1005 1008 1010 1025 1029 1031 --o lh.parietal.nii.gz sysname Darwinhostname iMac-di-Stefano.localmachine x86_64user Stefano input aparc+aseg.mgzframe 0nErode3d 0nErode2d 0output lh.parietal.nii.gzBinarizing based on matching valuesnMatch 6 0 1005 1 1008 2 1010 3 1025 4 1029 5 1031binval 1binvalnot 0mghRead(/Applications/freesurfer/subjects//Control20/aparc+aseg.mgz, -1): could not open file Thanks Regards, Stefano

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Displaying clusters from different QDEC analyses, overlapped
by Tudor Popescu 03 Oct '14

03 Oct '14

Dear FS list, I have significant clusters from several QDEC analyses (each one for a different DV< i.e. thickness, area, etc). I would like to generate a picture of a standard brain (talairach or MNI) with several of these clusters superimposed on the same brain, to show where there are e.g. regions of increased thickness and of decreased volume. I thought I could just load a standard brain in FreeView and then add the MGH files corresponding to all my contrasts of interest (after they've been MonteCarlo-corrected), in order to view all my clusters on the same brain. However, when I load any *mc-z.abs.th13.sig.cluster.mgh *in FreeView, the image seems to be blank, although in QDEC it shows a large blue cluster. I played around with the Min/Max/Level values in FreeView, but that didn't help. Can anyone suggest how to accomplish this? Thanks! Tudor

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Re: [Freesurfer] mri_glmfit and volume visuals‏
by Martin Reuter 03 Oct '14

03 Oct '14

Hi Taylor, for plotting stats, you need to use an external program (e.g. a bar plot in spreadsheet, or in matlab). Often people report effects and p-values in a table but bar plots or box plots may be visually more appealing. Pct. Change of global brain: the global brain volume is reported in the header of the stats files in freesurfer and should be part of the table produced in your second command? Note that the total brain volume in freesurfer is not directly estimated but is the sum of some structures, minus some others (e.g. ventricles). Because of that it may not be one of the most reliable measures that FS reports. Probably looking at WM volume and total GM volume is better. Best, Martin On 10/03/2014 12:42 PM, Taylor North wrote: > Hello Freesurfer community, > > I am using the mri_glmfit model to analyze my group data at two time > points. First I ran the following commanded swapping pc1 with spc to > get an image of the symmetrized percent change across my group. > > ------------------------------------------------------------------------------------------------------------------------- > long_mris_slopes --qdec long.testretest.qdec \ > --meas thickness \ > --hemi lh \ > --sd $SUBJECTS_DIR \ > --do-pc1 --do-label \ > --generic-time \ > --fwhm 15 \ > --qcache fsaverage \ > --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \ > --isec-labels lh.testretest.fsaverage.cortex.label > > mri_glmfit --osgm \ > --glmdir lh.testretest.thickness-pc1.fwhm15 \ > --y lh.testretest.thickness-pc1.stack.fwhm15.mgh \ > --label lh.testretest.fsaverage.cortex.label \ > --surf fsaverage lh > > tksurfer fsaverage lh pial -overlay > lh.testretest.thickness-pc1.fwhm15/osgm/sig.mgh > --------------------------------------------------------------------------------------------------------------------------------------- > > Next I ran the following command to get volume change results: > > ---------------------------------------------------------------------------------------------------------------------------------------- > > long_stats_slopes --qdec long.testretest.qdec \ > --stats aseg.stats \ > --meas volume \ > --sd $SUBJECTS_DIR \ > --do-pc1 \ > --generic-time \ > --stack-pc1 testretest.aseg-pc1.stack.txt > > mri_glmfit --osgm \ > --glmdir testretest.aseg-pc1 \ > --table testretest.aseg-pc1.stack.txt > > cat testretest.aseg-pc1/sig.table.dat > > ---------------------------------------------------------------------------------------------------------------------------------------------- > > The results from the volume command are all in a table which is useful > however I was wondering if there also is anyway to get a visual > picture of the percent volume changes like the first spc command provided? > > Also is there any command that can give you the percent change in > global brain volume? > > > Thanks for the help! > > Cheers, > > Taylor North -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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Re: [Freesurfer] A question about spherical registration
by Reza Rajimehr 03 Oct '14

03 Oct '14

Hi Doug, Step 1 did not generate "/iter00/lh.reg.template.tif" - though there was no obvious error for that on the screen. Not sure if this happened because of not having an annot file for mris_make_template. Here is what I saw on the screen: %%%%%%%%%% /usr/local/freesurfer/bin/make_average_surface --subjects F99 --out iter00 --template-only --surf-reg sphere $Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp $ Wed Oct 1 23:00:55 EDT 2014 /home/reza/structurals setenv SUBJECTS_DIR /home/reza/structurals/ output ddir is /home/reza/structurals/ uid=1000(reza) gid=1000(reza) groups=1000(reza),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),108(lpadmin),124(sambashare) ==================== make_average_surface ==================== Wed Oct 1 23:00:56 EDT 2014 /home/reza/structurals /usr/local/freesurfer/bin/make_average_surface --subjects F99 --out iter00 --template-only --surf-reg sphere input subjects: F99 output subject: iter00 mri_add_xform_to_header -c auto /home/reza/structurals//iter00/mri/mni305.cor.mgz /home/reza/structurals//iter00/mri/mni305.cor.mgz INFO: extension is mgz #@# Making lh registration template --------- /home/reza/structurals/iter00 mris_make_template -norot -annot aparc lh sphere F99 lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization... processing subject F99 (1 of 1) reading spherical surface /home/reza/structurals//F99/surf/lh.sphere... could not read annot file /home/reza/structurals//F99/surf/../label/lh.aparc.annot No such file or directory mris_make_template: could not read annot file aparc No such file or directory ERROR: cannot find /home/reza/structurals//iter00/lh.reg.template.tif ERROR: cannot find /home/reza/structurals//iter00/lh.reg.template.tif ERROR: cannot find /home/reza/structurals//iter00/lh.reg.template.tif %%%%%%%%%% Reza Hi Reza, I think that this should work. doug set subjectlist = (subject1 subject2 ...) 1. Create a template from a single subject make_average_surface --subjects $subjectlist[1] \ --out iter00 --template-only --surf-reg sphere.reg 2. Register each subject to this template, including first subject. Each of these may take 30 min, so, if you have a lot of subjects, you may want to submit each job to the cluster. foreach subject ($subjectlist) # Create subject/surf/iter00.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter00 --no-annot end 3. Create a new template from all subjects using the new registration make_average_surface --subjects $subjectlist \ --out iter01 --template-only --surf-reg iter00.sphere.reg 4. Register each subject to this new template foreach subject ($subjectlist) # Create subject/surf/iter01.sphere.reg, --no-annot for monkey surfreg --s $subject --t iter01 --no-annot end 5. Return to step 3. Iterate 4 or 5 times to remove the dependence on the first subject. When using mri_surf2surf or mris_preproc, spec --surfreg iterXX.sphere.reg. For mris_preproc also spec --targ iterXX

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White matter segmentation
by Leise Borg 03 Oct '14

03 Oct '14

Hi FreeSurfer I need the white matter segmentations, and I've looked at some e-mail correspondence and one answer I think I can use is the following: If you just want white matter, then better to create a mask from the aparc+aseg.mgz with mri_binarize with the --wm flag. doug I just don't understand what it means.. I do have the aparc+asset.mgz, but what is a mri_binarize and --wm flag? I don't have FreeSurfer installed on my on computer. All the best, Leise.

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Re: [Freesurfer] White matter and white matter lesions
by Douglas N Greve 03 Oct '14

03 Oct '14

Hi Leise, please copy the list on all emails. Thanks. You can use the matlab textread command (specify to use # as the comment) doug On 10/03/2014 02:48 AM, Leise Borg wrote: > > Hi Douglas > > Thanks a lot for your answer. I will definitely do that. Can you tell > me how I load this aseg.stats file into Matlab? I do not have > FreeSurfer downloaded on my own computer. Do I need that to load this > file? > > -Leise. > > Why not just use the values in aseg.stats? > > On 10/01/2014 07:44 AM, Leise Borg wrote: > > > > > > Hi FreeSurfer > > > > > > I am working on a project concerning Alzheimer’s patients and I need > > > to know the positions of white matter (WM) and white matter lesions > > > (WML) from your segmentations. > > > > > > To find the WML, I use label 77 in the aparc.a2009s+aseg.mgz-files. > > > > > > To find the WM, I use labels 2 and 41 in the ribbon.mgz-files and > > > subtract the ventricles by subtracting labels: 4, 5 14, 15, 43 44 > > > found in the aseg.mgz-files. > > > > > > However, in the two sets of positions – one for WML and one for WM > > > –there is an overlap. It is not big, but it is there. > > > > > > Can you help me finding the true WML- and WM-segmentations? > > > > > > With kind regards, Leise. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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