[Freesurfer] recommended WM lesion filling procedure?
Hi, I have a bunch of scans from patients with mulitple sclerosis. Since they all have substantial t2w hyperintensities I would like to automate the process of WM filling and re-running. Looking through the emails and the wiki, however, I am a bit confused. http://www.freesurfer.net/fswiki/FsTutorial/ControlPoints says I should NOT use control points for white matter lesions: "Control points should NOT be used to try and normalize a brain lesion to 110. Such defects should be fixed with white matter edits" BUT, http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes says I should: "mris_make_surfaces: where wm lesions exist, even if the lesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. A potential work-around is to set lesion voxels in brainmask.mgz and norm.mgz to 110 and lesions voxels in aseg.mgz to 77 (lesion mask can be derived manually or from an automated algorithm), then run recon-all -autorecon2-cp." I'm assuming that the guidance in the release notes supersedes the other wiki page but I wanted to make sure. thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was 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.
Re: [Freesurfer] qdec cannot find subjects in qdec.table.dat
Hi, I am also having the same problems. Was this ever resolved? I run freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 on ubuntu hardy 2.6.24-18. thanks, mishkin On Wed, Sep 10, 2008 at 12:55 PM, David Qixiang Chen <[EMAIL PROTECTED] > wrote: > Hi, > I'm running freesurfer in Ubuntu hardy 2.6.24-19 > > I've ran into a problem with loading data tables in qdec. > I've followed the instructions in tutorial 2a and created associated data > tables, but qdec always returned the error: > ERROR: QdecProject::VerifySubjects: Couldn't find subject '' in > SUBJECTS_DIR > sh: Syntax error: Bad fd number > > I've even tried to load the tutorial example files, and had the same errors > returned back to me, > please assist: > > Here's the error output: > Loading data table > /media/STORAGE/buckner_data/tutorial_subjs/group_analysis_tutorial/qdec/qdec.table.dat... > Number of columns: 189 > fsid column:1 > Number of factors: 188 > Number of subjects: 40 > Reading discrete factor levels from config file > /media/STORAGE/buckner_data/tutorial_subjs/group_analysis_tutorial/qdec/gender.levels...'Male','Female', > done. > > Data table > /media/STORAGE/buckner_data/tutorial_subjs/group_analysis_tutorial/qdec/qdec.table.dat > loaded. > sh: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '004' in > SUBJECTS_DIR > sh: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '008' in > SUBJECTS_DIR > sh: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '017' in > SUBJECTS_DIR > sh: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '021' in > SUBJECTS_DIR > sh: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in > SUBJECTS_DIR > sh: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '039' in > SUBJECTS_DIR > sh: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '040' in > SUBJECTS_DIR > sh: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '045' in > SUBJECTS_DIR > sh: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '049' in > SUBJECTS_DIR > sh: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '067' in > SUBJECTS_DIR > sh: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '073' in > SUBJECTS_DIR > sh: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '074' in > SUBJECTS_DIR > > > Thanks > > - David Qixiang Chen > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] qdec.table.dat error
Hi, When I try to load a qdec.table.dat I always get the same error: sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in SUBJECTS_DIR I've tried digging around through the archives and still can't seem to find a solution for this problem. I've tried tcsh and the bash shell. Here is a bit more information and my qdec.table.dat is attached. Any ideas on how to get qdec up and running would be very useful. thanks, mishkin FREESURFER_HOME: /lab1/FreeSurfer/4.0.5/quarantine Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 Debian version: lenny/sid Kernel info: Linux 2.6.24-18-generic x86_64 opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> qdec & opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> Reading /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/tkUtils.tcl Using /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/fsgdfPlot.tcl Loading data table /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/qdec.table.dat... Setting SUBJECTS_DIR to '/lab1/FreeSurfer/4.0.5/ms-mni/testing' Number of columns: 4 fsid column:1 Number of factors: 3 Number of subjects: 2 Reading discrete factor levels from config file /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/gender.levels...'Male','Female', done. Data table /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/qdec.table.dat loaded. SUBJECTS_DIR is '/lab1/FreeSurfer/4.0.5/ms-mni/testing' sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester2' in SUBJECTS_DIR Error loading the data table. qdec.table.dat Description: MOPAC data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] qcache commands
Hi, I am trying to understand what happens when you run the recon-all -qcache command I noticed these three commands get run: mris_preproc --s tester2 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh mri_surf2surf --hemi lh --srcsubject tester2 --surfreg sphere.reg --sval /lab1/FreeSurfer/4.0.5/ms-mni/testing/tester2/surf/lh.thickness --sfmt curv --trgsubject fsaverage --tval ./tmp.mris_preproc.12176/tester2.1.mgh --noreshape mri_concat ./tmp.mris_preproc.12176/tester2.1.mgh --o lh.thickness.fsaverage.mgh My questions are: 1. Am I right to assume that the first command (mris_preproc) is just a wrapper script that calls the 2nd and 3rd commands? 2a. In the case above, does the 3rd command (mri_concat) simply copy the contents of tester2.1.mgh into lh.thickness.fsaverage.mgh. 2b. Is there a case when mri_concat will actually concat more than one thing into lh.thickness.fsaverage.mgh? thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec.table.dat error
Hi Nick, I tried unalias -a and then runnig qdec but it didn't work either. I think the problem is with bash vs. sh in ubuntu (possible all debian systems). ie. /bin/sh is not the same as /bin/bash so not all bash commands will work. I did this: sudo mv /bin/sh /bin/sh.bak sudo ln -s /bin/bash /bin/sh and then it worked. I'm hoping this doesn't have repercussion for my other programs though. thanks, mishkin On Tue, Oct 7, 2008 at 11:20 PM, Nick Schmansky <[EMAIL PROTECTED]> wrote: > yes, this sounds like a tough one. the VerifySubjects routine that > produces that error message just runs the 'ls' command on that subject > directory name, so that is why i asked. if you run the 'ls' command on > '/lab1/FreeSurfer/4.0.5/ms-mni/testing/tester', does it return a correct > response? ie a non-zero status? > > what does 'which ls' say? possibly it is aliased to something that is > causing a problem. > > does qdec work despite the error? the code is setup to just print the > error, but continue anyway. if the subject doesnt exist, it will fail > downstream (during mri_glmfit). > > i'll try to think of other things. > > nick > > > On Tue, 2008-10-07 at 21:26 -0400, Mishkin Derakhshan wrote: >> Hi Nick, >> Yes I've checked most of the obvious things I could think of. >> The directories all exist, permissions on all files are 775, i will >> try 777 but don't suspect that will make a difference. >> My env variables seem to be set properly as well. >> >> opus[/lab1/FreeSurfer/4.0.5/ms-mni/testing/tester]$ . >> /lab1/FreeSurfer/4.0.5/quarantine/SetUpFreeSurfer.sh >> freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /lab1/FreeSurfer/4.0.5/quarantine >> FSFAST_HOME /lab1/FreeSurfer/4.0.5/quarantine/fsfast >> FSF_OUTPUT_FORMAT nii >> SUBJECTS_DIR /lab1/FreeSurfer/4.0.5/ms-mni/testing/ >> MNI_DIR /lab1/FreeSurfer/4.0.5/quarantine/mni >> >> I get the same error when trying to load the tutorial qdec.table.dat as well. >> >> My analysis is stuck at this point so any help is greatly appreciated. >> >> thanks, >> mishkin >> >> >> On Tue, Oct 7, 2008 at 7:27 PM, Nick Schmansky >> <[EMAIL PROTECTED]> wrote: >> > Mishkin, >> > >> > Does this directory exist? >> > >> > /lab1/FreeSurfer/4.0.5/ms-mni/testing/tester >> > >> > The error message you are seeing is checking for the existence of that >> > directory. >> > >> > Nick >> > >> > >> > On Tue, 2008-10-07 at 14:30 -0400, Mishkin Derakhshan wrote: >> >> Hi, >> >> When I try to load a qdec.table.dat I always get the same error: >> >> >> >> sh: Syntax error: Bad fd number >> >> ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in >> >> SUBJECTS_DIR >> >> >> >> I've tried digging around through the archives and still can't seem to >> >> find a solution for this problem. >> >> I've tried tcsh and the bash shell. >> >> Here is a bit more information and my qdec.table.dat is attached. Any >> >> ideas on how to get qdec up and running would be very useful. >> >> thanks, >> >> mishkin >> >> >> >> >> >> FREESURFER_HOME: /lab1/FreeSurfer/4.0.5/quarantine >> >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 >> >> Debian version: lenny/sid >> >> Kernel info: Linux 2.6.24-18-generic x86_64 >> >> >> >> opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> qdec & >> >> opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> >> >> Reading /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/tkUtils.tcl >> >> >> >> Using /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/fsgdfPlot.tcl >> >> >> >> Loading data table >> >> /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/qdec.table.dat... >> >> Setting SUBJECTS_DIR to '/lab1/FreeSurfer/4.0.5/ms-mni/testing' >> >> Number of columns: 4 >> >> fsid column:1 >> >> Number of factors: 3 >> >> Number of subjects: 2 >> >> Reading discrete factor levels from config file >> >> /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/gender.levels...'Male','Female', >> >> done. >> >> >> >> Data table /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/qdec.table.dat >> >> loaded. >> >> SUBJECTS_DIR is '/lab1/FreeSurfer/4.0.5/ms-mni/testing' >> >> sh: Syntax error: Bad fd number >> >> ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in >> >> SUBJECTS_DIR >> >> sh: Syntax error: Bad fd number >> >> ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester2' in >> >> SUBJECTS_DIR >> >> Error loading the data table. >> >> ___ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> >> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qcache commands
Thanks.
Just as a follow up. What is the format of lh.thickness.fsaverage.mgh?
Is this how I would view the entire contents of it:
mri_convert --ascii lh.thickness.fsaverage.mgh lh.thickness.fsaverage.mgh.asc
And am I right in assuming that the contents of this file, are my
thickness stats of my subject, after being aligned to fsaverage space,
and that each line is in the correct order that corresponds to each
vertex in fsaverage/surf/lh.{pial,white} ?
mishkin
On Tue, Oct 7, 2008 at 7:36 PM, Nick Schmansky
<[EMAIL PROTECTED]> wrote:
> Mishkin,
>
> Yes, mris_preproc is a wrapper script that calls mris_vol2surf,
> mris_surf2surf and mri_concat. You can view mris_preproc in a text
> editor.
>
> In answer to 2a, in this case tester2.1.mgh should be the same as
> lh.thickness.fsaverage.mgh. In answer to 2b, one file is always
> 'concatenated', as mris_preproc is used by the -qcache. In other usages
> of mris_preproc, it is possible to concatnate multiple files.
>
> Nick
>
>
> On Tue, 2008-10-07 at 17:16 -0400, Mishkin Derakhshan wrote:
>> Hi,
>> I am trying to understand what happens when you run the recon-all
>> -qcache command
>> I noticed these three commands get run:
>>
>> mris_preproc --s tester2 --hemi lh --meas thickness --target fsaverage
>> --out lh.thickness.fsaverage.mgh
>>
>> mri_surf2surf --hemi lh --srcsubject tester2 --surfreg sphere.reg
>> --sval /lab1/FreeSurfer/4.0.5/ms-mni/testing/tester2/surf/lh.thickness
>> --sfmt curv --trgsubject fsaverage --tval
>> ./tmp.mris_preproc.12176/tester2.1.mgh --noreshape
>>
>> mri_concat ./tmp.mris_preproc.12176/tester2.1.mgh --o
>> lh.thickness.fsaverage.mgh
>>
>> My questions are:
>> 1. Am I right to assume that the first command (mris_preproc) is just
>> a wrapper script that calls the 2nd and 3rd commands?
>> 2a. In the case above, does the 3rd command (mri_concat) simply copy
>> the contents of tester2.1.mgh into lh.thickness.fsaverage.mgh.
>> 2b. Is there a case when mri_concat will actually concat more than one
>> thing into lh.thickness.fsaverage.mgh?
>>
>> thanks,
>> mishkin
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
>
___
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[Freesurfer] lh.thickness file format
Hi, I have my own stats files that I would like to incorporate into the freesurfer stream, if possible. Ie. after running FreeSurfer, I create a ?h.mystats (containing something like image intensities for example), where the format of ?h.mystats is just an ascii file, where each line is the value at that vertex. What I ultimately want to do, is to transform ?h.mystats into fsaverage space, that way I can compare ?h.mystats across subjects. I was hoping I could use the given sphere.reg which has already been calculated to do this. I renamed ?h.mystats to ?h.thickness and tried the following which I think will work: mris_preproc --s mysubject --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh But it complains that: Reading curvature file /lab1/FreeSurfer/4.0.5/ms-mni/testing//tester/surf/lh.thickness MRISreadBinaryCurvature: incompatible vertex number in file /lab1/FreeSurfer/4.0.5/ms-mni/testing//tester/surf/lh.thickness I checked and I have the same number of lines in my file as vertices on my object so my questions are: 1. Do I have to convert my ascii ?h.mystats to a curvature (binary) file like ?h.thickness, and if so how does one do this? 2. Is this the right way to get what I ultimately want to do, or is there another method? thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all -long questions
Hi, I have a couple questions regarding the -long option. 1) The longitudinal instructions listed in recon-all -help all use recon-all -all -long. If I am only interested in the subcortical segmentation, will the longitudinal processing still work if I only use recon-all -subcortseg ? 2) How long does the longitudinal pipeline take for a) tp1, which has already had the cross-sectional workflow run b) tp2, which gets compared to tp1. I suspect a) and b) are the same, but do they take the same amount of time as a conventional cross sectional run? thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Segmentation Volume Data
Hi, Are the details of the partial volume corrections described anywhere on the wiki, I couldn't find anything? Is it just a certain percentage of the volume that is disregarded depending on the surface area, or is there a probabilistic labeling of the structures somewhere? Is it possible to get a mask of the structure that includes the partial volume correction, or one of the probabilistic labels (if such a thing exists)? thanks, mishkin On Tue, Nov 25, 2008 at 1:22 PM, Doug Greve <[EMAIL PROTECTED]> wrote: > The aseg.stats is computed with a partial volume correction at the > boundaries of the structures, tkmedit just counts voxels. > > Yuan Xu wrote: > > Hi FreeSurfer: > > > > when I compare a brain structure volume count on the aseg.stats files > with a volume of same structure measured using tkmedit "Segmentation Label > Volume Count" feature to display on TkMedit Tools window. They are closer > but not the same, usually about 3 to 10% difference. Why? > > > > Thanks, > > > > Yuan > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] postmortem data
Hi, I have three questions regarding some postmortem data at high resolution (0.35 mm^3 isotropic). 1) A question was asked about the possibility of using postmortem scans in freesurfer back in sept 2007 and Bruce said: >Not easily, although we have some tools for doing this. They aren't packaged and distributed though. Any updates? 2) Is there a way to take advantage of this resolution and not resample to the 1mm^3 grid? 3) I only have one hemisphere. I am trying to flip the hemisphere to create a whole brain that can be used as input, but seeing as most of the pipeline splits things up into two hemispheres, is there a way to run Freesurfer with just one hemisphere from the start? thanks in advance as always, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] What is the transformation from surfaces vertices to volume voxel coordinates?
Hi Lloyd,
I dealt with the same problem at one time. My input volume was a minc
volume but I imagine the procedure should work for your input as well.
for native.mnc, which was your input into freesurfer, do this command:
mri_info --cras native.mnc
my output was
-2.35588 52.7907 24.8145
Then you can create the following transformation matrix:
1 0 0 -2.35588
0 1 0 52.7907
0 0 1 24.8145
0 0 0 1
You can then transform each co-ordinate point in your surface with the
above transformation matrix and then your surfaces will be in what the
MNI calls
world co-cordinate space (these are referred to as "scanner RAS" on the
freesurfer wiki coordinate page).
Overlaying this new surface with my native.mnc worked for me.
mishkin
On Thu, Feb 19, 2009 at 5:17 PM, Douglas N Greve
wrote:
> what are you trying to do? If you're trying to bring the surface coords into
> talairach (mni305) space, then you can use mri_surf2surf with the
> --sval-xyz-tal orig --taval-xyz options.
>
> Lloyd Elliott wrote:
>>
>> I am trying to overlay surface information acquired with freesurfer on to
>> the original MRI volume. I tried reading lh.orig with [vertices,faces] =
>> freesurfer_read_surf('surf/lh.orig') and then transforming the vertices
>> with the matrix:
>>
>> vertices_affine = [vertices' ; ones(1,size(vertices,1))] # append the
>> affine coordinates
>> overlay = (rsb2vox*inv(M)) * vertices_affine
>>
>> where
>>
>> M = xfm_read('mri/transforms/talairach.xfm')
>>
>> and
>>
>> rsb2vox = inv([
>> [-1 0 0 128 ;
>> 0 0 1 -128;
>> 0 -1 0 128;
>> 0 0 0 1]
>> ])
>>
>> I was lead to believe that this is the correct procedure by reading the
>> 'official' description of the coordinate systems on the freesurfer wiki (
>> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems ). Unfortunately
>> the scaling and translation is incorrect. I've also tried other
>> permutations of the above matrix multiplication without any luck. Am I
>> doing something incorrectly?
>>
>> Thanks,
>> Lloyd Elliott
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
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[Freesurfer] masking out ROIs on the surface
Hello list, I would like to create a mask on fsaverage/surf/?h.pial that masks out the areas where the surface does not follow the cortex, but is just cutting across the mid line or across the brain stem. I know Freesurfer does this to maintain the surface toplogy, and I think it only does this in these two areas. Does a simple txt file with n vertices and a 0 or 1 value at each vertex exist somewhere? Has anyone on the list bothered to label this area manually and would be willing to share? thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] masking out ROIs on the surface
Thanks. After reading up on the wiki it seems that a more general solution I'm loking for would be to somehow get the contents of ?h.aparc.annot into ascii form. I know mris_annotation2label will kind of do this, but it creates one file for every label. What I'm loooking for is a single file with n rows corresponding to the n vertices in ?h.pial, and then next to each one, a number representing what label it belongs to (or what value to look up in the LUT). can this be done somehow, or at the very least can I get the contents of ?h.*.annot into ascii format so I can manipulate things. thanks, mishkin On Tue, Apr 7, 2009 at 1:05 PM, Bruce Fischl wrote: > Hi Mishkin, > > yes, the ?h.cortex.label should be created for every subject that labels the > cortical regions of the surface. > > cheers, > Bruce > On Tue, 7 Apr 2009, Mishkin Derakhshan wrote: > >> Hello list, >> I would like to create a mask on fsaverage/surf/?h.pial that masks out >> the areas where the surface does not follow the cortex, but is just >> cutting across the mid line or across the brain stem. I know >> Freesurfer does this to maintain the surface toplogy, and I think it >> only does this in these two areas. >> Does a simple txt file with n vertices and a 0 or 1 value at each >> vertex exist somewhere? Has anyone on the list bothered to label this >> area manually and would be willing to share? >> thanks, >> mishkin >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] masking out ROIs on the surface
Hi Nick, I was recently trying to redo something you had helped me out with back in April (see below), but I now get this error: ERROR: Option --seg unknown The wiki page still says this option exists, but I'm guessing is outdated https://surfer.nmr.mgh.harvard.edu/fswiki/mri_annotation2label#Detailsfor.27seg.27outputfilelabelnumbers Was this option deprecated at some point? Could you send me a version where this works, or is there another way, I can get what I'm after: >> to somehow get the contents of >> ?h.aparc.annot into ascii form. I know mris_annotation2label will kind >> of do this, but it creates one file for every label. What I'm loooking >> for is a single file with n rows corresponding to the n vertices in >> ?h.pial, and then next to each one, a number representing what label >> it belongs to (or what value to look up in the LUT). thanks, mishkin On Wed, Apr 8, 2009 at 4:19 PM, Nick Schmansky wrote: > Mishkin, > > This will create what you want: > > cd subj/label > mri_annotation2label --subject subj \ > --hemi lh \ > --annotation aparc \ > --seg lh.aparc.mgh > > replacing subj and lh with appropriate. > > then type: > > mris_convert -c ./lh.aparc.mgh \ > ../surf/lh.white \ > lh.aparc.asc > > and the output file (lh.aparc.asc) will have lines like this: > > 71586 -39.60123 -13.37572 -34.24242 1007.0 > > which are: > > vno X Y Z labelno > > where labelno is found in $FREESURFER_HOME/FreeSurferColorLUT.txt, for > instance 1007 is ctx-lh-fusiform > > Nick > > > > On Tue, 2009-04-07 at 17:00 -0400, Mishkin Derakhshan wrote: >> Thanks. After reading up on the wiki it seems that a more general >> solution I'm loking for would be to somehow get the contents of >> ?h.aparc.annot into ascii form. I know mris_annotation2label will kind >> of do this, but it creates one file for every label. What I'm loooking >> for is a single file with n rows corresponding to the n vertices in >> ?h.pial, and then next to each one, a number representing what label >> it belongs to (or what value to look up in the LUT). >> can this be done somehow, or at the very least can I get the contents >> of ?h.*.annot into ascii format so I can manipulate things. >> >> thanks, >> mishkin >> >> >> On Tue, Apr 7, 2009 at 1:05 PM, Bruce Fischl >> wrote: >> > Hi Mishkin, >> > >> > yes, the ?h.cortex.label should be created for every subject that labels >> > the >> > cortical regions of the surface. >> > >> > cheers, >> > Bruce >> > On Tue, 7 Apr 2009, Mishkin Derakhshan wrote: >> > >> >> Hello list, >> >> I would like to create a mask on fsaverage/surf/?h.pial that masks out >> >> the areas where the surface does not follow the cortex, but is just >> >> cutting across the mid line or across the brain stem. I know >> >> Freesurfer does this to maintain the surface toplogy, and I think it >> >> only does this in these two areas. >> >> Does a simple txt file with n vertices and a 0 or 1 value at each >> >> vertex exist somewhere? Has anyone on the list bothered to label this >> >> area manually and would be willing to share? >> >> thanks, >> >> mishkin >> >> ___ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >> > >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] masking out ROIs on the surface
Hi,
I'm not sure whether the --seg option ever got looked into, but for
those searching the lists in the future, here is the quick hack I used
in perl to accomplish what I wanted:
mishkin
#! /usr/bin/perl
if($ARGV <1){
print "\nUsage: $0 \n";
print "Assumes SUBJECTS_DIR is set, and mri_annotation2label is in
your path\n";
print "WIll output ?h.annot.asc, which has the names of the
parcellations, and\n"
print "WIll output ?h.annot.txt, which has the number of the
parcellations [1-35]\n"
exit(1);
}
$name = $ARGV[0];
$DIR = $ENV{'SUBJECTS_DIR'};
@structures = qw(bankssts caudalanteriorcingulate caudalmiddlefrontal
corpuscallosum cuneus entorhinal frontalpole fusiform inferiorparietal
inferiortemporal isthmuscingulate lateraloccipital
lateralorbitofrontal lingual medialorbitofrontal middletemporal
paracentral parahippocampal parsopercularis parsorbitalis
parstriangularis pericalcarine postcentral posteriorcingulate
precentral precuneus rostralanteriorcingulate rostralmiddlefrontal
superiorfrontal superiorparietal superiortemporal supramarginal
temporalpole transversetemporal unknown);
@sides = qw(lh rh);
foreach $hemi(@sides){
my @master;
system("mri_annotation2label --subject ${name} --hemi ${hemi}
--outdir ${DIR}/${name}/label/");
$i=0;
foreach $reg(@structures){
$i = $i+1; #index number of each label
open(FIN,"${DIR}/${name}/label/${hemi}.${reg}.label");
$line = ; #header
$line = ; #header
while($line = ){
my @array = split(/ /,$line);
my $vertex = $array[0]; #get the vertex number
$master[${vertex}] = "${reg} $i";
}
close(FIN);
}
open(FASC,"> ${DIR}/${name}/label/${hemi}.annot.asc");
open(FTXT,"> ${DIR}/${name}/label/${hemi}.annot.txt");
foreach $element(@master){
my @array = split(/ /,$element);
print FASC "$array[0]\n"; #names
print FTXT "$array[1]\n"; #number
}
close(FASC);
close(FTXT);
}
On Thu, Nov 5, 2009 at 9:14 PM, Mishkin Derakhshan wrote:
> Hi Nick,
> I was recently trying to redo something you had helped me out with
> back in April (see below), but I now get this error:
> ERROR: Option --seg unknown
>
> The wiki page still says this option exists, but I'm guessing is outdated
> https://surfer.nmr.mgh.harvard.edu/fswiki/mri_annotation2label#Detailsfor.27seg.27outputfilelabelnumbers
>
> Was this option deprecated at some point? Could you send me a version
> where this works, or is there another way, I can get what I'm after:
>
>>> to somehow get the contents of
>>> ?h.aparc.annot into ascii form. I know mris_annotation2label will kind
>>> of do this, but it creates one file for every label. What I'm loooking
>>> for is a single file with n rows corresponding to the n vertices in
>>> ?h.pial, and then next to each one, a number representing what label
>>> it belongs to (or what value to look up in the LUT).
>
> thanks,
> mishkin
>
> On Wed, Apr 8, 2009 at 4:19 PM, Nick Schmansky
> wrote:
>> Mishkin,
>>
>> This will create what you want:
>>
>> cd subj/label
>> mri_annotation2label --subject subj \
>> --hemi lh \
>> --annotation aparc \
>> --seg lh.aparc.mgh
>>
>> replacing subj and lh with appropriate.
>>
>> then type:
>>
>> mris_convert -c ./lh.aparc.mgh \
>> ../surf/lh.white \
>> lh.aparc.asc
>>
>> and the output file (lh.aparc.asc) will have lines like this:
>>
>> 71586 -39.60123 -13.37572 -34.24242 1007.0
>>
>> which are:
>>
>> vno X Y Z labelno
>>
>> where labelno is found in $FREESURFER_HOME/FreeSurferColorLUT.txt, for
>> instance 1007 is ctx-lh-fusiform
>>
>> Nick
>>
>>
>>
>> On Tue, 2009-04-07 at 17:00 -0400, Mishkin Derakhshan wrote:
>>> Thanks. After reading up on the wiki it seems that a more general
>>> solution I'm loking for would be to somehow get the contents of
>>> ?h.aparc.annot into ascii form. I know mris_annotation2label will kind
>>> of do this, but it creates one file for every label. What I'm loooking
>>> for is a single file with n rows corresponding to the n vertices in
>>> ?h.pial, and then next to each one, a number representing what label
>>> it belongs to (or what value to look up in the LUT).
>>> can this be done somehow, or at the very least can I get the contents
>>> of ?h.*.annot into ascii format so I can manipulate things.
>>>
>>> thanks,
>>> mishkin
>>>
>>>
&g
[Freesurfer] colin27 skullstrip problem
Hi, I'm trying to get the surfaces for the colin27 brain that is included with the mni packages. Has anyone managed to do this before? I thought I would have an easy time given that this linear average of 27 brains has very good signal to noise and nice contrasts, and even though recon-all completes without errors, the surfaces are way off. The main problem appears to be the skull stripping. My input volume is here: http://opus.bic.mni.mcgill.ca/public/colin27_t1_tal_lin.mnc.gz These are the steps I took and where I think the problem might be: 1. gunzip colin27_t1_tal_lin.mnc.gz 2. recon-all -i colin27_t1_tal_lin.mnc -subjid colin27 3. tkmedit conlin27 orig/001.mgz At this point the image the brightness and contrast levels of the image look very washed out. I am hoping this is only a display issue and that the underlying intensities of the image are still intact and is not a result of something going on in mri_convert, but maybe this is what is causing the downstream skull strip to fail. Can someone take a look? http://opus.bic.mni.mcgill.ca/public/001.mgz 4. recon-all -autorecon1 -subjid colin27 5. tkregister2 --mgz --s colin27 --fstal Results are not perfect but reasonable ie. about the same as many other runs I've had that have passed so I don't think it is the registration. 6. tkmedit colin27 brainmask.mgz -aux T1.mgz It is clear this is where the problem is. http://opus.bic.mni.mcgill.ca/public/brainmask.mgz http://opus.bic.mni.mcgill.ca/public/T1.mgz 7. I have subsequently tried: recon-all -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -subjid colin27 (basically extract the entire head) recon-all -skullstrip -wsthresh 5 -clean-bm -no-wsgcaatlas -subjid colin27 (basically extracted the entire head) recon-all -skullstrip -wsthresh 5 -clean-bm -subjid colin27 (extracted the brain, but left large chunks of skull) recon-all -skullstrip -wsthresh 2 -clean-bm -subjid colin27 (extracted the brain, but left quite a few chunks of skull) I'm concerned that the -wsthresh is so low in order to get a reasonable result, that's why I think the intensities might be off (see step 3). I'm re-running -autorecon2/3 now to see if the surfaces are better, but if someone could take a look at my input file and the converted 001.mgz to see if it isn't a problem there it would be much appreciated. thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] colin27 skullstrip problem
Hi Bruce, A copy of the surfaces would be much appreciated. Just let me know where I can download them from. Ideally if you can tar the whole colin27 directory so I have the aseg and aparc info as well that would be great. I think including this and/or the mni152 and average_305 surfaces would be great, though this might bloat the size of the download. Not sure if you had a chance to look at my files, but do you think the problem I have is just a bad skullstrip, or is it an intensity issue from the conversion? thanks, mishkin On Mon, Nov 30, 2009 at 8:53 PM, Bruce Fischl wrote: > Hi Mishkin, > > yes, I generates surfaces for the Colin27 dataset. It actually doesn't have > great gray/white contrast, probably due to differential B0 distortions in > the different sessions. Maybe we should include it as part of our release? > In any case, I can send it to you. > > cheers > Bruce > > > On Mon, 30 Nov 2009, Mishkin Derakhshan wrote: > >> Hi, >> I'm trying to get the surfaces for the colin27 brain that is included >> with the mni packages. Has anyone managed to do this before? >> >> I thought I would have an easy time given that this linear average of >> 27 brains has very good signal to noise and nice contrasts, and even >> though recon-all completes without errors, the surfaces are way off. >> The main problem appears to be the skull stripping. >> >> My input volume is here: >> http://opus.bic.mni.mcgill.ca/public/colin27_t1_tal_lin.mnc.gz >> >> These are the steps I took and where I think the problem might be: >> 1. gunzip colin27_t1_tal_lin.mnc.gz >> 2. recon-all -i colin27_t1_tal_lin.mnc -subjid colin27 >> 3. tkmedit conlin27 orig/001.mgz >> At this point the image the brightness and contrast levels of the >> image look very washed out. I am hoping this is only a display issue >> and that the underlying intensities of the image are still intact and >> is not a result of something going on in mri_convert, but maybe this >> is what is causing the downstream skull strip to fail. Can someone >> take a look? >> http://opus.bic.mni.mcgill.ca/public/001.mgz >> 4. recon-all -autorecon1 -subjid colin27 >> 5. tkregister2 --mgz --s colin27 --fstal >> Results are not perfect but reasonable ie. about the same as many >> other runs I've had that have passed so I don't think it is the >> registration. >> 6. tkmedit colin27 brainmask.mgz -aux T1.mgz >> It is clear this is where the problem is. >> http://opus.bic.mni.mcgill.ca/public/brainmask.mgz >> http://opus.bic.mni.mcgill.ca/public/T1.mgz >> 7. I have subsequently tried: >> recon-all -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -subjid >> colin27 (basically extract the entire head) >> recon-all -skullstrip -wsthresh 5 -clean-bm -no-wsgcaatlas -subjid >> colin27 (basically extracted the entire head) >> recon-all -skullstrip -wsthresh 5 -clean-bm -subjid colin27 (extracted >> the brain, but left large chunks of skull) >> recon-all -skullstrip -wsthresh 2 -clean-bm -subjid colin27 (extracted >> the brain, but left quite a few chunks of skull) >> >> I'm concerned that the -wsthresh is so low in order to get a >> reasonable result, that's why I think the intensities might be off >> (see step 3). >> >> I'm re-running -autorecon2/3 now to see if the surfaces are better, >> but if someone could take a look at my input file and the converted >> 001.mgz to see if it isn't a problem there it would be much >> appreciated. >> >> thanks, >> mishkin >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] subject to fsaverage
Hi, I am looking for the transformation matrix that takes my input volume (orig.mgh) and maps it into the same space as fsaverage (or the inverse of this transformation if it already exists). I've already run recon-all -all, and -qcache, so I'm pretty sure this information exists somewhere, but after searching through the data, the wiki and the mailing list, I'm embarrassed to say that I still can't find it. If this information hasn't been stored, I imagine mri_surf2surf can calculate it for me. Would this be the best way? thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] error testing freesurfer installation
Hi, I just installed the rh9 version of fressurfer. I am running Ubuntu 6.10. I had the libtiff.so.3 error, which I seemed to have fixed by just making a sym link to libtiff.so.4 ( I hope that is okay). Now I get this error about the aseg.mgz.gz not existing. It looks like it isn't looking in the mri/ dir as it should be. [EMAIL PROTECTED]:/usr/local/freesurfer$ tkmedit bert norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt libGL warning: 3D driver claims to not support visual 0x5b Talairach transform /autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /usr/local/freesurfer/subjects/bert/mri/transforms/talairach.xfm zcat: /usr/local/freesurfer/subjects/bert//aseg.mgz.gz: No such file or directory mghRead(/usr/local/freesurfer/subjects/bert//aseg.mgz, -1): read error Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl These are the only things i've added to my .bashrc : export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh which produces this output: freesurfer-Linux-rh9-stable-pub-v3.0.5 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast SUBJECTS_DIR/usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni GSL_DIR /usr/local/freesurfer/lib/gsl FSL_DIR /usr/local/freesurfer/fsl Did I forget to set a variable somewhere? thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Coordinate Systems
Hi, I am new to FreeSurfer and even after having read the wiki, I have a few questions regarding the coordinate systems. 1. What coordinate system do the final surfaces have. ie. mris_convert rh.pial rh.pial.ascii will list the coordinates in what space? 2. Are the coordinates of T1.mgz and rh.pial for example the same, or does tkmedit compute transforms on the fly so that everything is aligned properly when you view it. 3. What transform (or combination of transforms) will get me from the final surfaces coordinates, to the MNI talairach like space (which I think is called avg305). many thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] subcortical segmentation
Hi, I am interested in just obtaining the subcortical segmentation labels and not generating surfaces. I would like to do this in as little time as possible and since I am only looking for label volumes (ie. hippocampal volumes) i figured that there must be some steps I can leave out of -autorecon2. Can anyone tell me the flags I should set to get the fastest way to generate these label files? I found: autorecon-all -subcortseg -subjid on the wiki, but it says this may take 11+ hours to complete so I thought I would just check before I batched things to run. many thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] subcortical segmentation
Hi, After running the -subcortseg option, i see the output volumes of certain structures on the screen. Are they stored anywhere in a text file? I checked stats/aseg.stats, and while the column headers indicate that there should be values for NVoxels and Volume_mm3, in the table those two fields are blank for all labels. Is this a bug, or is there another option I need to set to get those fields filled in? thanks, mishkin On 6/1/07, Doug Greve <[EMAIL PROTECTED]> wrote: unfortunately, you have to go thru the segmentation as that is part of the surface-based stream. doug David Perlman wrote: > On this topic, if I *don't* want subcortical segmentation, but rather > only surface generation and thickness maps, what's the best option to > use for that? It seems like it might be -noaseg, but I couldn't find > any references to this flag being used with human data, only with non- > human primates, so I thought I'd ask before I assumed I'd figured it > out. > > On Jun 1, 2007, at 1:49 PM, Bruce Fischl wrote: > >> yes, sorry. The subcortical segmentation is early in the processing >> stream, and pretty much the slowest step. > > > -- > -dave > Science arose from poetry... when times change the two can meet again > on a higher level as friends. -Göthe > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] subcortical segmentation
Very embarrassing. I thought the column headings were 1. Col 2.Headers 3.Index 4.SegId as that is how they lined up in my text editor. Now I realize that the fourth column is indeed my volume. sorry for all the confusion. mishkin On 6/5/07, Doug Greve <[EMAIL PROTECTED]> wrote: what do you mean? The 3rd and 4th columns have that info: # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 1 00.0 Left-Cerebral-Exterior 0. 0. 0. 0. 0. 2 2263489 263489.0 Left-Cerebral-White-Matter 107.2167 8.761952. 140.88. 3 3245645 245645.0 Left-Cerebral-Cortex 86.619410.803413. 132. 119. 4 4 5227 5227.0 Left-Lateral-Ventricle 46.789313.392218.92.74.0000 Mishkin Derakhshan wrote: Hi Jenni, thanks for the reply. The log file says it finished without any eroors. In the aseg.stats file, none of the structures have the NVoxels of Volume_mm3 reported. I attached the file so you can see what I mean. I am using freesurfer-Linux-rh9-stable-pub-v3.0.5 on debian sarge. I ran another subject as well and my aseg.stats file appears to be the same. The command lines I ran were: recon-all -i hippo_test_subject1_t1g_nu.mnc -autorecon1 -subjid subject1 recon-all -subcortseg -subjid subject1 did I miss anything? thanks, mishkin On 6/5/07, Jenni Pacheco <[EMAIL PROTECTED]> wrote: Hi Mishkin, Are all the fields blank in the aseg.stats table, or just for some things? It shouldn't be like this. It may be that there are some structures listed in that file that are not labeled in the aseg and then reported as a zero, but it shouldn't be all of them. Were there any error messages at the end of this particular subject's scripts/recon-all.log? Jenni On Tue, 5 Jun 2007, Mishkin Derakhshan wrote: > Hi, > After running the -subcortseg option, i see the output volumes of > certain structures on the screen. Are they stored anywhere in a text > file? > I checked stats/aseg.stats, and while the column headers indicate that > there should be values for NVoxels and Volume_mm3, in the table those > two fields are blank for all labels. Is this a bug, or is there > another option I need to set to get those fields filled in? > thanks, > mishkin > > > On 6/1/07, Doug Greve <[EMAIL PROTECTED]> wrote: >> unfortunately, you have to go thru the segmentation as that is part of >> the surface-based stream. >> >> doug >> >> David Perlman wrote: >> >> > On this topic, if I *don't* want subcortical segmentation, but rather >> > only surface generation and thickness maps, what's the best option to >> > use for that? It seems like it might be -noaseg, but I couldn't find >> > any references to this flag being used with human data, only with non- >> > human primates, so I thought I'd ask before I assumed I'd figured it >> > out. >> > >> > On Jun 1, 2007, at 1:49 PM, Bruce Fischl wrote: >> > >> >> yes, sorry. The subcortical segmentation is early in the processing >> >> stream, and pretty much the slowest step. >> > >> > >> > -- >> > -dave >> > Science arose from poetry... when times change the two can meet again >> > on a higher level as friends. -Göthe >> > >> > >> > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [EMAIL PROTECTED] >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> In order to help us help you, please follow the steps in: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Ubuntu and freesurfer
I am currently running freesurfer on Ubuntu, so yes! Ubuntu runs Debian linux, so you can just follow the instructions for a debian install located on the wiki (ie. use the Red Hat 9 download): http://surfer.nmr.mgh.harvard.edu/fswiki/Download mishkin p.s. Perhaps Ubuntu can be added to the list on the wiki under Notes. On 8/27/07, lan lin <[EMAIL PROTECTED]> wrote: > Can freesurfer be installed in Ubuntu? > > thanks > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert options
Hi, I am having troubles getting the right options with mri_convert. I ran: recon-all -autorecon1 -i original.mnc -s subj1 recon-all -subcortseg -s subj1 I now want to convert aseg.mgz into aseg.mnc but in the same space and with the same orientation as my original.mnc file. My original.mnc file has the following attributes: double zspace ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:step = -0.9765625 ; zspace:start = 127.418768256005 ; zspace:direction_cosines = -0.0275245718714001, -0.00051469764711, 0.999620994692302 ; double yspace ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:step = -0.9765625 ; yspace:start = 146.850463958339 ; yspace:direction_cosines = -0.0186971433325, 0.999825193136882, -2.319984599e-08 ; double xspace ; xspace:comments = "X increases from patient left to right" ; xspace:step = 1.46 ; xspace:start = -95.4780255890689 ; xspace:direction_cosines = 0.999446254069973, 0.0186900576545041, 0.0275293837630133 ; short image(zspace, yspace, xspace) ; Any help would be much appreciated. thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert options
Thanks. It didn't quite work as I'm guessing the step sizes in original.mnc are negative, but I am able to reshape the minc file afterwards to get it exactly the same. >From my (limited) understanding of mri_vol2vol, when you invoke it with the --regheader is it taking the ras to voxel transform as listed from mri_info aseg.mgz and then applying that to the image to get into the original.mnc space? thanks, mishkin On Dec 13, 2007 11:47 PM, Nick Schmansky <[EMAIL PROTECTED]> wrote: > Mishkin, > > try this: > > mri_vol2vol --mov aseg.mgz \ > --targ original.mnc \ > --o aseg-in-native.mnc \ > --regheader \ > --interp nearest > > Nick > > > On Thu, 2007-12-13 at 22:05 -0500, Mishkin Derakhshan wrote: > > Hi, > > I am having troubles getting the right options with mri_convert. > > > > I ran: > > recon-all -autorecon1 -i original.mnc -s subj1 > > recon-all -subcortseg -s subj1 > > > > I now want to convert aseg.mgz into aseg.mnc but in the same space and > > with the same orientation as my original.mnc file. > > > > My original.mnc file has the following attributes: > > double zspace ; > > zspace:comments = "Z increases from patient inferior to superior" ; > > zspace:step = -0.9765625 ; > > zspace:start = 127.418768256005 ; > > zspace:direction_cosines = -0.0275245718714001, > > -0.00051469764711, 0.999620994692302 ; > > double yspace ; > > yspace:comments = "Y increases from patient posterior to anterior" ; > > yspace:step = -0.9765625 ; > > yspace:start = 146.850463958339 ; > > yspace:direction_cosines = -0.0186971433325, 0.999825193136882, > > -2.319984599e-08 ; > > double xspace ; > > xspace:comments = "X increases from patient left to right" ; > > xspace:step = 1.46 ; > > xspace:start = -95.4780255890689 ; > > xspace:direction_cosines = 0.999446254069973, 0.0186900576545041, > > 0.0275293837630133 ; > > short image(zspace, yspace, xspace) ; > > > > Any help would be much appreciated. > > thanks, > > mishkin > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] right choroid plexus missing
Hi, Is there any reason why aseg.stats only has a label for the left-choroid-plexus (id 31) and none for the right? I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hardware
Hi, I currently run a CPU with 2 Intel(R) Xeon(R) CPU X5355 @ 2.66GHz with 16GB RAM, and a single instance of recon-all -all with version freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 takes this long: real1219m45.802s user1218m32.345s sys 2m1.152s Which is about 20.5 hours. In my experience, on an older CPU with a single dual quad core Xeon @ 1.6Ghz, a single instance of recon-all -all took this long: real1806m53.356s user1797m35.349s sys 7m59.934s Which is about 30 hours. Perhaps a benchmark page can be set up on the wiki, where people can record how long recon-all -all took for one subject. For example CPU-MODEL CPU-FREQ RAM FREESURFER-VERSION TIME just a suggestion, mishkin On Jan 2, 2008 7:16 AM, Thomas Doering <[EMAIL PROTECTED]> wrote: > > > Hi, > we are buying a new Computer for running Freesurfer, FSL etc. > After my experience, that a 3 GHz xeon 5050 was running slower than a 1.6 > GHz Xeon 5110, due to older processor architecture, i wanna be sure to buy > the right one. > Does somebody has an experience with a Xeon E 5345, 2.66 GHz ? > If so, how long does a Freesurfer recon-all process run? > > Thanks for any suggestions, > Thomas > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] surface co-ordinates
Hi, 1. When using mris_convert lh.white lh.white.ascii, what co-oridnate system are the xyz co-ordinates reported in? ie. is it the RAS co-ordinates of the T1.mgz volume? 2. I am making the assumption that the lh.white and the lh.pial will always have the same number of indices and polygons. Can I also make the assumption that the order in which they are printed using mris_convert will be the same. ie. Will the vertex on line 54 of lh.white.ascii correspond to the same vertex on line 54 of lh.pial.ascii? thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] surface co-ordinates
On Wed, Feb 20, 2008 at 10:46 PM, Doug Greve <[EMAIL PROTECTED]> wrote: > On Wed, 20 Feb 2008, Mishkin Derakhshan wrote: > > > Hi, > > > > 1. When using mris_convert lh.white lh.white.ascii, what co-oridnate > > system are the xyz co-ordinates reported in? ie. is it the RAS > > co-ordinates of the T1.mgz volume? > > These are "surface RAS" or "tkregister RAS". There is a power point > presentation on coord systems on the wiki. So according to the overview on https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems if I wanted to go from the SurfaceRAS (ie. what the lh.white.ascii is in) back to the coord system of my original volume, i would transform my object with the matrix M = inv(xform3)*inv(xform2)*inv(xform1) ? The diagram leads me to believe this is the same as M = inv(4)*inv(1) ? The text also says the SurfaceRasFromVoxel matrix is: [ 3x3 part (t1 - c_r)] [ same as(t2 - c_a)] [ xform0 (t3 - c_s)] [0 1 ] So the inverse of that would be what I'm looking for as well right? In that case, what is xform0? Just my directional cosines of the original image? Would t1,t2,t3 =0 then? thanks for the help, mishkin > > > > > 2. I am making the assumption that the lh.white and the lh.pial will > > always have the same number of indices and polygons. Can I also make > > the assumption that the order in which they are printed using > > mris_convert will be the same. ie. Will the vertex on line 54 of > > lh.white.ascii correspond to the same vertex on line 54 of > > lh.pial.ascii? > > Yes. > > doug > > > thanks, > > mishkin > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] WM mask
HI Antonio, You can use mris_convert to get the surfaces into ascii format. ie: mris_convert lh.white lh.white.ascii If you look at the file you see the following: #!ascii version of lh.white 126302 252600 -7.101086 -100.61 -1.796945 0 -7.231718 -99.740860 -1.915022 0 . . -7.355780 53.003563 -9.506091 0 0 1 2 0 3 2 1 0 . . 120678 121091 121102 0 122524 122217 122525 0 The first line is a comment. The second line lists the number of points and then the number of polygons. The next 126302 lines (number of points) list the x y z co-ordinates of that point. The last 252600 lines (number of polygons) list the points that make up that polygon. hope that helps, mishkin On Thu, Feb 21, 2008 at 1:48 PM, Gallo, Antonio (NIH/NINDS) [F] <[EMAIL PROTECTED]> wrote: > Dear all, > > We are trying to extract a cerebral white matter mask from the > Freesurfer output. > We are currently using the aparc+aseg file in order > to do this, however we realized that the white matter mask (taken by > choosing the voxels with values equal to 2 and 41) doesn't correspond > exactly to the white matter we would like to have, which rather would > follow the WM boundary obtained with the surface processing. > Is there a way to get a more accurate mask that corresponds to these > boundaries? > Also, is there a description of the file format that the surface files > are written in? > > Thank you, > > Antonio > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] inflation and registration to a sphere
Hi, After reading the wiki and the references on the wiki, specifically [1] and [2], I'm still a little confused about how the inflation and registration to a sphere occurs. ie. what energy functions are being minimized at each step. I think it is a 3 step process, where 1. Surfaces are inflated by minimizing the energy function Js. This creates ?h.inflated. Js = 1/2V (EE ||xi-xn||^2) + lambda-d*Jd (8) in [1] 2. The inflated surfaces are then projected to a sphere by minimizing the energy function J. This creates ?h.sphere J = ??? 3. The sphere is registered to the average by minimizing the energy function J. This creates ?h.sphere.reg. J = Jp + lambda-d*Jd + lambda-a*Ja (5) in [2] Is there a step I am missing? Are my energy functions correct? thanks, mishkin [1] Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System, Fischl, B., Sereno, M.I., Dale, A.M., (1999). NeuroImage, 9(2):195-207. [2] High-resolution inter-subject averaging and a coordinate system for the cortical surface, Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999). ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Calling mri_convert from Java code
Hey Alex,
Just from looking at the first two lines of your environment variables
I think you might have forgot the 's' on Applications for
FREESURFER_HOME.
>>>
String[] env = {"FREESURFER_HOME=/Application/freesurfer",
"FSFAST_HOME=/Applications/freesurfer/fsfast",
mishkin
On Mon, Feb 25, 2008 at 6:13 PM, Alexander Zaitsev (CNI)
<[EMAIL PROTECTED]> wrote:
> Hello:
>
> I need to call mri_convert utility from Java code.
> The problem is when I am making a system call, I am getting the
> following error :
> >
> FreeSurfer license file /Application/freesurfer/.license not found.
> If you are outside the NMR-Martinos center,
>go to http://surfer.nmr.mgh.harvard.edu to
>get a valid license file (it's free).
> If you are inside the NMR-Martinos center,
>make sure to source the standard environment.
> <<
>
> The mri_convert runs from the shell without problem and the .license
> file is in the right directory.
>
> I am including the following env variables into the system call:
> >>>
>String[] env = {"FREESURFER_HOME=/Application/freesurfer",
>"FSFAST_HOME=/Applications/freesurfer/fsfast",
>"SUBJECTS_DIR=/Applications/freesurfer/subjects",
>"MNI_DIR=/Applications/freesurfer/mni",
>"GSL_DIR=/Applications/freesurfer/lib/gsl",
>"FSL_DIR=/Applications/freesurfer/fsl",
>"FUNCTIONALS_DIR=$FREESURFER_HOME/sessions",
>"FSLOUTPUTTYPE=NIFTI_GZ", sPATH, "DISPLAY=:0.0", "HOME=/tmp",
>"DYLD_LIBRARY_PATH=/Applications/freesurfer/lib/gsl/lib",
>"MINC_BIN_DIR=/Applications/freesurfer/mni/bin",
>"MINC_LIB_DIR=/Applications/freesurfer/mni/lib",
>"MNI_DATAPATH=/Applications/freesurfer/mni/data",
>"LOCAL_DIR=/Applications/freesurfer/local",
>"FMRI_ANALYSIS_DIR=/Applications/freesurfer/fsfast",
>
> "MNI_PERL5LIB=/Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6",
>
>
> "PERL5LIB=/Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6",
>"LD_LIBRARY_PATH=/Applications/freesurfer/lib/gsl/lib",
>"FSLDIR=/Applications/freesurfer/fsl",
>"FSL_BIN=/Applications/freesurfer/fsl/bin",
>"FSLTCLSH=/Applications/freesurfer/fsl/bin/tclsh",
>"FSLWISH=/Applications/freesurfer/fsl/bin/wish",
>"FSLGNUPLOT=/Applications/freesurfer/fsl/bin/gnuplot",
>"FSLDISPLAY=/Applications/freesurfer/fsl/bin/display",
>"FSLCONVERT=/Applications/freesurfer/fsl/bin/convert",
>"FSLBROWSER=/Applications/freesurfer/fsl/tcl/fslwebbrowser",
>"FSLCONFDIR=/Applications/freesurfer/fsl/config"
>};
>
> <<<
>
>
> Am I missing something?
>
> Yes, the mri_convert runs fine when called from the shell.
> And I don't see any other env variables related to the free surfer.
>
> Thank you,
>
> Alex
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error while loading shared libraries:libtiff.so.3
Hi Lucia, I ran into the problem as well. For me, just making a symbolic link named libtiff.so.3 which points to libtiff.so.4 seemed to do the trick. Try this: ln /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3 (assumes your libs are in /usr/lib/) hope that helps, mishkin On Sat, Mar 29, 2008 at 9:16 AM, Lúcia Garrido <[EMAIL PROTECTED]> wrote: > Hello, > > I'm using Debian and downloaded > freesurfer-Linux-centos4-stable-pub-v4.0.2-full.tar.gz. > > Everything worked fine when I tested the installation with tkmedit and > tksurfer. > I then ran > recon-all -i C04_SS.nii -autorecon1 -s C04_SS > and it also finished without errors. > > But when I ran recon-all -autorecon2 -s C04_SS, > there was an error at the end saying: > mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot > open shared object file: No such file or directory > > I've checked the shared libraries and I have libtiff.so.4. Could you let me > know > how to get libtiff.so.3 to work and if I should do something else? > > Thank you very much. > > Lucia > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical surface in MNI space?
Hi David, I use both the MINC world and the freesurfer world. One thing which may be of use to you or others, is to get from the surface co-ordinates, back to world-coordinates (or "scanner RAS"), so that minc tools etc. display things properly. To do this, you need to apply a simple translation. ie. for native.mnc which was your input into freesurfer do this command: mri_info --cras native.mnc my output was -2.35588 52.7907 24.8145 Then you can create the following transformation matrix: 1 0 0 -2.35588 0 1 0 52.7907 0 0 0 24.8145 0 0 0 1 If you then convert your surfaces to ascii: mris_convert lh.pial lh.pial.asc You can then transform each co-ordinate point in lh.pial.asc with the above transformation matrix and then your surfaces will be in MNI world co-cordinates. (these are referred to as "scanner RAS" on the freesurfer wiki coordinate page). >From there, if you have a transformation that already maps your subject to mni152, then you can apply that transformation. I think annother way, would be to use the information provided in: $FREESURFER_HOME/average/mni152.register.dat. I'm assuming lines 5-9 of that file are a transformation that will move you from mni152 space to fsaverage (avg305) space. (though im not sure if that is moving you from a SurfaceRAS to SurfaceRAS space or just from RAS to RAS or what?) If FreeSurfer calculates the transformation matrix required to get from your subject space(native, or RAS, or SurfaceRAS) to fsaverage (RAS or SurfaceRAS) space, then you could probably combine those transformations to get what you want. Unfortunately, I don't have a good enough grasp of the coordinate system yet to guide you through this process. Perhaps Doug can guide me in the right direction? If you are interested in any of the other things, feel free to contact me as I have some tools to convert FreeSurfer outputs to MINC outputs (.mnc, .obj). hope that helps, mishkin On Mon, Apr 14, 2008 at 11:52 AM, Doug Greve <[EMAIL PROTECTED]> wrote: > > > Rather than creating a subject in mni152 space, you can map your 152 data > to our fsaverage (mni305) with $FREESURFER_HOME/average/mni152.register.dat, > eg > > tkmedit fsaverage T1.mgz -overlay yourstats152.nii \ >-overlay-reg $FREESURFER_HOME/average/mni152.register.dat > > or > > tksurfer fsaverage lh inflated -overlay yourstats152.nii \ >-overlay-reg $FREESURFER_HOME/average/mni152.register.dat > > doug > > > > Stark, David Ernest wrote: > > > > Hi all, > > I am new to Freesurfer and would like to generate a cortical (pial) surface > of 1 subject's brain, but I need the surface in MNI 152 space (this is for > display purposes, so that I can overlay clusters already in MNI space). What > is the best way to accomplish this? I already have the subject's freesurfed > output (if any of those files can be of use). Also, if a pial surface > already exists for one of the standard brains out there, that would also be > of use. > > Thanks! > David > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] vertex correspondence
Hi, I know that at some point in the pipeline, the surfaces are registered to a common sphere, and thus I'm hopping there is a one-to-one vertex correspondance between subjects. My question is, let's say I look at vertex X, on subject1, how do I find out the corresponding vertex location on subjectN. thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ASEG atlas modality
Hi, >From what I read here: https://surfer.nmr.mgh.harvard.edu/fswiki/AsegOptimization The atlas has is made from 27 data sets (14 GE, 13 SIEMENS). Can you give a bit more info about the sequences used. ie were they FLASH-based or MPRAGE. Are these 27 data sets available for download somewhere? thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] 3mm slices?
Hi, I'm wondering if anyone has looked at the accuracy/reproducibility of cortical thickness measurements using 3mm slice data. I found the Han 2006 paper in NeuroImage comparing different sequences, but it doesn't compare different slice thicknesses. If not, does anyone have anecdotal experience using 3mm slices? thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was 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.
[Freesurfer] wm edits to fix memory error
I don't think this made it through to the list the first time... Hi, Like others on the list I got the ran out of memory error, which seems to be the result of a gross error somewhere: CORRECTING DEFECT 1 (vertices=109084, convex hull=14490) Excessive topologic defect encountered: could not allocate 649386741 edges for retessellation Cannot allocate memory Linux bach 2.6.24-27-server #1 SMP Fri Mar 12 01:23:09 UTC 2010 x86_64 GNU/Linux recon-all -s freesurfer_results exited with ERRORS at Thu Sep 9 22:15:45 EDT 2010 Anyway, it looks like my skull strip is okay, but my wm.mgz and thus my filled.mgz files are where I have the gross errors. It looks like a lot of WM voxels are missing, and not just due to lesions. Skull: http://imgur.com/hJO5U.jpg WM: http://imgur.com/r6nGT.jpg Filled: http://imgur.com/LanJS.jpg My questions is, should I just fix the WM using this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits, or is this a problem at the normalization step, or is there something else I can try? thanks, mishkin p.s i tired using 4.5.0 and 5.0.0 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was 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.
[Freesurfer] qdec with custom paths?
Hi, My data is not in the usual SUBJECTS_DIR/fsid structure. 1. Is it possible to run qdec so that it loads each subject from a full path instead of expecting them all to be under the same SUBJECTS_DIR? ie. with something like this: qdec.table.dat path_to_fsid gender age /full/path/fsid1 Male 23 /full/otherpath/fsid2 Female 27 2. If not, do you think creating a new common subjects dir and then using symbolic links will work? 3. If not, would I have to copy the entirety of the directory, or do I only need a select few subdirs like the surf/ and stats/ ? thanks, mishkin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was 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.
