Freesurfer December 2009

freesurfer@nmr.mgh.harvard.edu

77 participants
105 discussions

Re: [Freesurfer] a question about mris_ca_train
by Guang Zeng 21 Dec '09

21 Dec '09

Hello, there, If I have the label file of a ROI, and I want to convert the RAS coordinate of each vertex to volume index, which command I can use? Thanks! Guang > Date: Fri, 18 Dec 2009 14:18:44 -0500 > From: greve(a)nmr.mgh.harvard.edu > To: freesurfer_zg(a)hotmail.com > Subject: Re: [Freesurfer] a question about mris_ca_train > > I don't have any more suggestions except to play with the projection > fraction. You can load the data simultaneously in tkmedit and tksurfer, > click on a hole in tksurfer, then use the "Save/Go To Point" feature to > see in tkmedit why the surface does not pass through your label. > > doug > > Guang Zeng wrote: > > Hello, Doug, > > > > Thanks a lot for your suggestion, I added --projfrac 0.5 to my > > vol2surf command, > > the result looks much better now, but there are still some regions > > among ROIs have no label, > > please see the attached figure. > > > > Could you give some suggestions to fix this problem. > > Thanks a lot! > > Guang > > > > > Date: Thu, 17 Dec 2009 12:22:28 -0500 > > > From: greve(a)nmr.mgh.harvard.edu > > > To: freesurfer_zg(a)hotmail.com > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > When you run vol2surf, try specifying --projfrac 0.5 to sample in the > > > middle of the ribbon. > > > > > > doug > > > > > > Guang Zeng wrote: > > > > Hello, Doug, > > > > > > > > Fix that dimension dismtach problem now, and got my annot.file, but I > > > > still have problems, > > > > I attached the images which show my atals and annotation file loaded > > > > into tkmedit and tksurfer, the surface is > > > > broken. > > > > > > > > Could you tell me what I need to do? > > > > > > > > Thanks a lot! > > > > Guang > > > > > > > > > > > > > Date: Wed, 16 Dec 2009 18:05:03 -0500 > > > > > From: greve(a)nmr.mgh.harvard.edu > > > > > To: freesurfer_zg(a)hotmail.com > > > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > > > > > Load it again in tkmedit to make sure you have the color table > > right, > > > > > then re-run you mris_seg2annot command with your color table. > > > > > > > > > > doug > > > > > > > > > > Guang Zeng wrote: > > > > > > Hello, Doug, > > > > > > > > > > > > I am transfering my color lookup table to FreeSurfer ColorLUT > > now. It > > > > > > may need a little while. > > > > > > I load the a.anat.mgz using tkmedit and FreeSurfer lookup table, > > > > > > although the label and the colors looks a little bit > > > > > > strange, but all the other things look fine to me such as the > > > > > > segmentation results are registered pretty well. > > > > > > > > > > > > Could you tell me what I need to do next, once my color lookup > > table > > > > > > is ready, > > > > > > > > > > > > Thanks! > > > > > > Guang > > > > > > > > > > > > > Date: Wed, 16 Dec 2009 17:39:07 -0500 > > > > > > > From: greve(a)nmr.mgh.harvard.edu > > > > > > > To: freesurfer_zg(a)hotmail.com > > > > > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > > > > > > > > > First, work in the volume instead of the surface because the > > > > surface is > > > > > > > too hard to determine what is going on. Convert a.nii to the > > > > anatomical > > > > > > > space with > > > > > > > > > > > > > > mri_vol2vol --mov a.nii --reg > > > > > > > $FREESURFER_HOME/subjects/sub1/compare/register_raw.dat --interp > > > > > > > nearest --fstarg \ > > > > > > > --o $FREESURFER_HOME/subjects/sub1/mri/a.anat.mgz > > > > > > > > > > > > > > Then look at the output in tkmedit: > > > > > > > > > > > > > > tkmedit sub1 orig.mgz -surfs -seg a.anat.mgz YOURLUT > > > > > > > > > > > > > > where YOURLUT is a color lookup table for your segmentation > > > > (model it > > > > > > > using FreeSurferColotLUT.txt). > > > > > > > > > > > > > > let me know if that looks ok > > > > > > > > > > > > > > doug > > > > > > > > > > > > > > Guang Zeng wrote: > > > > > > > > Hello, Doug, > > > > > > > > > > > > > > > > Thanks a lot for your quick reply, I removed that "ico 7", > > now > > > > it is: > > > > > > > > > > > > > > > > mri_vol2surf --src a.nii --src_type nifti --srcreg > > > > > > > > $FREESURFER_HOME/subjects/sub1/compare/register_raw.dat > > --hemi > > > > rh --o > > > > > > > > ./atlas-rh.mgz --out_type mgh --float2int round --interp > > nearest > > > > > > > > > > > > > > > > and I rerun the two commands, it finished without problems. > > > > > > > > > > > > > > > > But I tried to take a look at this annotation file, I load > > the > > > > volume > > > > > > > > use tksurfer, then import my myatalas.annot, a multiple-line > > > > warning > > > > > > > > is showed as > > > > > > > > : Warning: vertex 132436 with annotation ffffffff - out of > > range! > > > > > > > > > > > > > > > > Could you give me some suggestions to fix it? > > > > > > > > > > > > > > > > The original input file I loaded into tksurfer has been > > converted > > > > > > into > > > > > > > > the anatomical space, and my first-command line input a.nii > > > > has been > > > > > > > > registered to it using tksurfer. > > > > > > > > > > > > > > > > Thanks a lot! > > > > > > > > Gaung > > > > > > > > > > > > > > > > > Date: Wed, 16 Dec 2009 17:12:50 -0500 > > > > > > > > > From: greve(a)nmr.mgh.harvard.edu > > > > > > > > > To: freesurfer_zg(a)hotmail.com > > > > > > > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > > > > > > > > > > > > > Sample it to the native subject's space with > > mri_vol2surf (not > > > > > > to ico > > > > > > > > > 7). Is the input file a.nii already in the anatomical space > > > > (ie, > > > > > > 256^3, > > > > > > > > > 1mm^3)? If not, make sure that your registration matrix is > > > > correct > > > > > > > > using > > > > > > > > > tkregister2. > > > > > > > > > > > > > > > > > > doug > > > > > > > > > > > > > > > > > > Guang Zeng wrote: > > > > > > > > > > Hello, Doug, > > > > > > > > > > > > > > > > > > > > Thanks a lot for your help, I am following your > > > > instruction now, > > > > > > > > > > > > > > > > > > > > First Step: mri_vol2surf > > > > > > > > > > my command line is > > > > > > > > > > mri_vol2surf --src a.nii --src_type nifti --srcreg > > > > > > > > > > $FREESURFER_HOME/subjects/sub1/compare/register_raw.dat > > > > --hemi > > > > > > rh --o > > > > > > > > > > ./atlas-rh.mgz --out_type mgh --float2int round > > > > --trgsubject ico > > > > > > > > > > --icoorder 7 --interp nearest > > > > > > > > > > > > > > > > > > > > Second step: mris_seg2annot > > > > > > > > > > my command line is > > > > > > > > > > mris_seg2annot --seg atlas-rh.mgz --ctab > > > > > > > > > > $FREESURFER_HOME/FreeSurferColorLUT.txt --s sub1 --h > > rh --o > > > > > > > > > > myatalas.annot > > > > > > > > > > > > > > > > > > > > But I got error like, > > > > > > > > > > ERROR: dimension mismatch. Surface has 132464 > > vertices, seg > > > > > > has 163842 > > > > > > > > > > Make sure the surface segmentation matches the subject > > and > > > > hemi > > > > > > > > > > > > > > > > > > > > Could you give me some suggestions to fix it? > > > > > > > > > > > > > > > > > > > > Thanks! > > > > > > > > > > Guang > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Date: Wed, 16 Dec 2009 13:12:59 -0500 > > > > > > > > > > > From: greve(a)nmr.mgh.harvard.edu > > > > > > > > > > > To: freesurfer_zg(a)hotmail.com > > > > > > > > > > > CC: freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > > > > > > > > > > > > > > > > > You can use mri_vol2surf with the --interp nearest > > > > option to > > > > > > sample > > > > > > > > > > your > > > > > > > > > > > volume segmentations onto the surface. You can then use > > > > > > > > mris_seg2annot > > > > > > > > > > > to convert this segmentation directly to an annotation, > > > > then use > > > > > > > > > > > mri_annotation2label to convert the annotation into a > > > > set of > > > > > > labels. > > > > > > > > > > > Nothing here guarantees that labels will be connected or > > > > > > > > contiguous nor > > > > > > > > > > > is it sure that all vertices on the surface will be > > labeled. > > > > > > > > > > > > > > > > > > > > > > doug > > > > > > > > > > > > > > > > > > > > > > Guang Zeng wrote: > > > > > > > > > > > > Hi, there, > > > > > > > > > > > > > > > > > > > > > > > > Recently, I sent sseveral emails to you to ask same > > > > kind of > > > > > > > > question > > > > > > > > > > > > about building our own template and atlas. > > > > > > > > > > > > Thanks a lot for your quick reply, they helps me a > > lot. > > > > > > > > > > > > > > > > > > > > > > > > Currently, I still have a question about building > > our own > > > > > > > > atlas using > > > > > > > > > > > > mris_ca_train, sorry to bother you again. > > > > > > > > > > > > > > > > > > > > > > > > We have a surface labeling atlas in our lab, we'd > > like to > > > > > > use this > > > > > > > > > > > > atlas instead of using FS's > > > > desikan_killiany.2007-06-20gcs. > > > > > > > > > > > > It is kind of difficult for us to load every subject > > > > in our > > > > > > > > training > > > > > > > > > > > > set to tksurfer, and manually label each ROI based > > on our > > > > > > ATLAS. > > > > > > > > > > > > > > > > > > > > > > > > What we try to do is: > > > > > > > > > > > > 1. Send each subject in the training set to our > > > > toolbox which > > > > > > > > will > > > > > > > > > > use > > > > > > > > > > > > our atlas to do surface labeling. For each subject > > it will > > > > > > > > output a > > > > > > > > > > > > file just like > > > > > > > > > > > > wmparc.mgz in FS, but it is NIfTI file. > > > > > > > > > > > > > > > > > > > > > > > > 2. Send each subject to FS pipeline to get the > > > > ?h.sphere.reg, > > > > > > > > ?h.sulc > > > > > > > > > > > > files. > > > > > > > > > > > > > > > > > > > > > > > > 3. Find a method to get my ?h. mylabels. annot files, > > > > and use > > > > > > > > > > > > mris_ca_train to build a new atlas. > > > > > > > > > > > > > > > > > > > > > > > > First of all, do you think what I try to do is > > reasonable? > > > > > > > > > > > > > > > > > > > > > > > > If yes, I know I need to get the FS .label files > > for each > > > > > > ROI, > > > > > > > > then I > > > > > > > > > > > > can call mris_label2annot to get ?h. mylabels. annot > > > > files. > > > > > > > > > > > > > > > > > > > > > > > > But how can I get the FS .label files for each ROI > > > > from our > > > > > > > > toolbox > > > > > > > > > > > > output ROI labeled NIfTI file? > > > > > > > > > > > > > > > > > > > > > > > > These qurstions trouble me for a long time, your > > help are > > > > > > really > > > > > > > > > > > > appreciate. > > > > > > > > > > > > > > > > > > > > > > > > Thanks a lot! > > > > > > > > > > > > Guang > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > > > Your E-mail and More On-the-Go. Get Windows Live > > > > Hotmail Free. > > > > > > > > > > Sign up > > > > > > > > > > > > now. > > <http://clk.atdmt.com/GBL/go/171222985/direct/01/> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > > > > 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: > > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > > > Freesurfer mailing list > > > > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > Your E-mail and More On-the-Go. Get Windows Live > > Hotmail Free. > > > > > > > > Sign up > > > > > > > > > > now. <http://clk.atdmt.com/GBL/go/171222985/direct/01/> > > > > > > > > > > > > > > > > > > -- > > > > > > > > > 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: > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > Hotmail: Trusted email with Microsoft’s powerful SPAM > > protection. > > > > > > Sign > > > > > > > > up now. <http://clk.atdmt.com/GBL/go/177141664/direct/01/> > > > > > > > > > > > > > > -- > > > > > > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > Hotmail: Free, trusted and rich email service. Get it now. > > > > > > <http://clk.atdmt.com/GBL/go/171222984/direct/01/> > > > > > > > > > > -- > > > > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > Hotmail: Free, trusted and rich email service. Get it now. > > > > <http://clk.atdmt.com/GBL/go/171222984/direct/01/> > > > > > > -- > > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > ------------------------------------------------------------------------ > > Hotmail: Powerful Free email with security by Microsoft. Get it now. > > <http://clk.atdmt.com/GBL/go/171222986/direct/01/> > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/

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in what space each subject has been processed following freesurfer pipeline
by Zhangyuanchao 21 Dec '09

21 Dec '09

Hi, there, Following the freesurfer pipeline, we can perform volume-based analysis and surface-based analysis. I would like to know in what space each subject has been processed. Is the processing of each subject in native space or standard space? When I say standard space, I mean stereotaxic space or something like that. For each subject, there is a file named "aseg.stats". Volume of subcortical structures are listed, I would like to know whether these volume are calculated in native or standard space. How could I obtain the volume of these structures in native and standard space respectively? Could anyone help me and give me some details? Thanks in advance. yuanchao ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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Hemispheric thickness as covariate
by Lena Palaniyappan 19 Dec '09

19 Dec '09

While attempting asymmetry analysis, I am planning to use hemisphere cortical mantle thickness as global covariate but how to arrive at this measure? The aparc algorithm does not give this value. Is there any code/script that I could use? Thanks in advance LKP _______________________________________________________ Lena Palaniyappan Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Re: [Freesurfer] QDEC
by Nick Schmansky 19 Dec '09

19 Dec '09

if the first run of asegstats2table to table worked, but the second failed, then that means that something is wrong with the stats data for subject 'test1' (or possibly something unusual with the way it was parsed). can you send me the aseg.stats files for both subjects. for the qcache command: recon-all -s <subjid> -qcache you need to run this for each subject. multiple subjects cannot be included on the command line. per your question on the meaning of 'concatenate into one file', this means that just prior to running mri_glmfit (which qdec does for you) it gathers the data (say, thickness) for each subject under study and combines into a single file. this is just an implementation thing (its easier to process with our software, rather than reading each file individually). n. On Sat, 2009-12-19 at 11:29 +0800, liyari5018 wrote: > Hi, > > Thanks for your reply, I tried to run > > > > asegstats2table --meas volume \ > --tablefile chen.out --subjects chen_yu_an > > > and then: > > > > asegstats2table --meas volume \ > --tablefile test1.out --subjects test1 > > The fisrst conmmand works, and another is failure. > > Report like this: > > --------------------------------------------------------------------- > > FREESURFER_HOME: /usr/local/freesurfer > > Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 > > Debian version: squeeze/sid > > Kernel info: Linux 2.6.31-14-generic i686 > > --------------------------------------------------------------------- > > 1) test1 chen_yu_an > > 2) > > lijin-desktop:/usr/local/freesurfer/subjects# python -V > > Python 2.6.4 > > ------------------------------------------------------------------------------------------------------ > > lijin-desktop:/usr/local/freesurfer/subjects# uname -a > > Linux lijin-desktop 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 > 14:04:26 UTC 2009 i686 GNU/Linux > > 3) > > ============================================================ > > lijin-desktop:/usr/local/freesurfer/subjects# asegstats2table --meas > volume --tablefile chen.out --subjects chen_yu_an > > /usr/local/freesurfer/bin/asegstats2table:5: DeprecationWarning: the > sets module is deprecated > > from sets import Set > > Building the table.. > > SUBJECTS_DIR : /usr/local/freesurfer/subjects > > Writing the table to chen.out > > ------------------------------------------------------------------------------------------------------ > > lijin-desktop:/usr/local/freesurfer/subjects# asegstats2table --meas > volume --tablefile test1.out --subjects test1 > > /usr/local/freesurfer/bin/asegstats2table:5: DeprecationWarning: the > sets module is deprecated > > from sets import Set > > Building the table.. > > SUBJECTS_DIR : /usr/local/freesurfer/subjects > > Traceback (most recent call last): > > File "/usr/local/freesurfer/bin/asegstats2table", line 406, in > <module> > > (rows, cols, table) = build_table(options) > > File "/usr/local/freesurfer/bin/asegstats2table", line 322, in > build_table > > table[statno+subname][segid] = > float(strlst[seg2statcol_map[o.meas]]) > > ValueError: invalid literal for float(): Volume_mm3 > > ======================================================= > > --------------------------------------------------------------------- > > Please include the following additional information in your report: > > 1) subject name > > 2) the entire command-line executed > > 3) the error message generated > > 4) optionally include the subject's /script/recon-all.log > > ----------------------------------------------------------------------- > > And one mroe quesitons: > > When I start Qdec befor, Qdec needs each subject to have pre-computed > smoothed data for the target surface (fsaverage is the default) for > each measure (thickness, sulc, area, curv, etc.), and in the > "pre-smoothed fsaverage surfaces" part , I CAN'T understand the > command: > > > > recon-all -s <subjid> -qcache > > The conmmand has three functions as the tutorial ppt show: > > 1\Resample into Common Space > > 2\Smooth > > 3\Concatenate into one file <<<<< What does this mean??? > > should I run this conmmand like this: > > # recon-all -s test1 -qcache > > # rcon-all -s chen_yu_an -qcache > > or like this: > > # recon-all -s test1 chen_yu_an -qcache > > > Thanks again for your reply! > > LJ > > > > > 在2009-12-19，"Nick Schmansky" <nicks(a)nmr.mgh.harvard.edu> 写道： > >from the error output shown, the problem appears to occur in the > >aparcstats2table script (line 322). its failing to parse a float. > > > >which version of freesurfer is being used? (type 'bugr' for this info) > >and which version of python? (type 'python -V') > > > >also, try running: > > > >asegstats2table --meas volume \ > > --tablefile test1.out --subjects test1 > > > >and then: > > > >asegstats2table --meas volume \ > > --tablefile chen.out --subjects chen_yu_an > > > >and see if either one works. i suspect either the aseg.stats file in > >one or the other is corrupted, or there's a problem with the python > >version on your system (its known to work with python v2.3.4). > > > >n. > > > > > > > >On Fri, 2009-12-18 at 19:12 +0800, liyari5018 wrote: > >> Hi all, > >> What's wrong with my QDEC? Today, I use the FeeSurfer Tutorial: > >> Surface Group Analysis with Qdec to analysis my data , when I > >> carried out to '' Stats Data Import'', I press the 'Generate Stats > >> Data Tables' button, but something happend to with a error(red > >> letters ): > >> > >> mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ > >> > >> ---------------------------------------------------------- > >> asegstats2table --meas volume > >> --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --subjects test1 chen_yu_an > >> /usr/local/freesurfer/bin/asegstats2table:5: DeprecationWarning: the > >> sets module is deprecated > >> from sets import Set > >> Building the table.. > >> SUBJECTS_DIR : /usr/local/freesurfer/subjects > >> Traceback (most recent call last): > >> File "/usr/local/freesurfer/bin/asegstats2table", line 406, in > >> <module> > >> (rows, cols, table) = build_table(options) > >> File "/usr/local/freesurfer/bin/asegstats2table", line 322, in > >> build_table > >> table[statno+subname][segid] = > >> float(strlst[seg2statcol_map[o.meas]]) > >> ValueError: invalid literal for float(): Volume_mm3 > >> ERROR: > >> In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWTkUtilities.cxx, line 230 > >> vtkKWQdecApp (0xa562cb8): > >> Script: > >> vtkTemp3 GenerateStatsDataTables > >> Returned Error on line 1: > >> Uncaught exception: command failed: asegstats2table --meas volume > >> --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --subjects test1 chen_yu_an > >> > >> Stack trace: > >> Uncaught exception: command failed: asegstats2table --meas volume > >> --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --subjects test1 chen_ yu_an > >> > >> while executing > >> "vtkTemp3 GenerateStatsDataTables" > >> > >> > >> What does this mean? How do I do to solve this ???? > >> > >> Thank you > >> > >> LJ > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

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Problem with aparcstats2table solved
by Jürgen Hänggi 19 Dec '09

19 Dec '09

Dear FS experts I solved the problem with aparcstats2table posted in my former email. The names of the parcellations derived from mris_make_face_parcellations are written with spaces in between ic3.tri face 1 ic3.tri face 2 Instead of ic3.tri_face_1 ic3.tri_face_2 Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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aparcstats2table problem
by Jürgen Hänggi 19 Dec '09

19 Dec '09

Dear FS experts I tried to get the cortical thickness of my own parcellations, but there is a problem. Although the whole information is available in the .stats file, only one value is written into the table file produced by aparcstats2table. I attached both one .stats file and the table file. I used the following command: aparcstats2table --subjects GCS_* --hemi lh --parc ic3.face --meas thickness --tablefile ic3_face_lh_thickness.txt Any idea? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Re: [Freesurfer] creating an atlas, mris_make_template
by Katherine Reiter 18 Dec '09

18 Dec '09

Bruce, I've redefined the precuneus on 10 subjects and I would like to somehow be able to incorporate my defintion of the precuneus in the recon stream to about 150 other subjects so I don't have to do it manually on each subject. I've made labels of the precuneus and moved neighboring ROIs to accommodate the difference. What would you suggest doing to make this possible? Thanks for your help, Katie On Fri, Dec 18, 2009 at 2:17 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Katie, > > what kind of atlas are you trying to make? If just a new parcellation you > don't need mris_make_temnplate or mris_register. You'll need to send us the > command lines if you have problems, otherwise it will be hard for us to > diagnose. > > cheers > Bruce > > > On Fri, 18 Dec 2009, Katherine Reiter wrote: > > Hello, >> >> I am in the process of making an atlas from 10 subjects. I'm unclear on >> the >> precise steps. So far I've made labels and annotation files for each >> subject. If I understand this process correctly the next steps would be >> and >> please correct me if I'm wrong: >> >> 1) mris_make template >> 2) mris_register >> 3) mris_sample_parc >> 4) mris_ca_train >> 5) mris_ca_label >> >> Right now I'm working on the mris_make_template command and I'm having >> some >> trouble with it. I keep getting this error message: >> >> >> lh.precuneus.template.tif: Deflate compression support is not configured. >> TiffWrite: TIFFWriteScanline returned error >> >> I researched the problem and it seems this problem is usually fixed by >> reconfiguring the libtiff to include deflate compression however we just >> reinstalled the libtiff to include suggested parameters, the zlib >> compression support is enabled. >> >> If anyone has any insight either in the mris_make_template problem or in >> the steps to making an atlas, it would be much appreciated! >> >> Thanks, >> >> Katie >> >>

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creating an atlas, mris_make_template
by Katherine Reiter 18 Dec '09

18 Dec '09

Hello, I am in the process of making an atlas from 10 subjects. I'm unclear on the precise steps. So far I've made labels and annotation files for each subject. If I understand this process correctly the next steps would be and please correct me if I'm wrong: 1) mris_make template 2) mris_register 3) mris_sample_parc 4) mris_ca_train 5) mris_ca_label Right now I'm working on the mris_make_template command and I'm having some trouble with it. I keep getting this error message: lh.precuneus.template.tif: Deflate compression support is not configured. TiffWrite: TIFFWriteScanline returned error I researched the problem and it seems this problem is usually fixed by reconfiguring the libtiff to include deflate compression however we just reinstalled the libtiff to include suggested parameters, the zlib compression support is enabled. If anyone has any insight either in the mris_make_template problem or in the steps to making an atlas, it would be much appreciated! Thanks, Katie

2 1

QDEC
by liyari5018 18 Dec '09

18 Dec '09

Hi all, What's wrong with my QDEC? Today, I use the FeeSurfer Tutorial: Surface Group Analysis with Qdec to analysis my data , when I carried out to '' Stats Data Import'', I press the 'Generate Stats Data Tables' button, but something happend to with a error(red letters ): mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ ---------------------------------------------------------- asegstats2table --meas volume --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --subjects test1 chen_yu_an /usr/local/freesurfer/bin/asegstats2table:5: DeprecationWarning: the sets module is deprecated from sets import Set Building the table.. SUBJECTS_DIR : /usr/local/freesurfer/subjects Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 406, in <module> (rows, cols, table) = build_table(options) File "/usr/local/freesurfer/bin/asegstats2table", line 322, in build_table table[statno+subname][segid] = float(strlst[seg2statcol_map[o.meas]]) ValueError: invalid literal for float(): Volume_mm3 ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0xa562cb8): Script: vtkTemp3 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: asegstats2table --meas volume --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --subjects test1chen_yu_an Stack trace: Uncaught exception: command failed: asegstats2table --meas volume --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --subjects test1 chen_yu_an while executing "vtkTemp3 GenerateStatsDataTables" What does this mean? How do I do to solve this ???? Thank you LJ

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Re: [Freesurfer] a question about mris_ca_train
by Guang Zeng 18 Dec '09

18 Dec '09

Hello, Doug, I convert the wmparc.mgz of a FS processed subject to a .nii file using mri_vol2vol and then use it to go through my command lines again, the created annotation file also have similar problem (please see the attached figs) , do I miss some refinement steps? My converted .nii file is called wmparc.nii, and my command line are: mri_vol2surf --src $FREESURFER_HOME/subjects/sub1/compare/wmparc.nii --src_type nifti --srcreg $FREESURFER_HOME/subjects/sub1/compare/register_raw.dat --hemi lh --o ./atlas-lh.mgh --out_type mgh --float2int round --interp nearest --projfrac 0.5 mris_seg2annot --seg atlas-lh.mgh --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --s sub1 --h lh --o myfsatalas.annot Then I load the annot file in tksurfer. Do I miss some refinement steps? Thanks a lot! Guang > Date: Thu, 17 Dec 2009 12:22:28 -0500 > From: greve(a)nmr.mgh.harvard.edu > To: freesurfer_zg(a)hotmail.com > Subject: Re: [Freesurfer] a question about mris_ca_train > > When you run vol2surf, try specifying --projfrac 0.5 to sample in the > middle of the ribbon. > > doug > > Guang Zeng wrote: > > Hello, Doug, > > > > Fix that dimension dismtach problem now, and got my annot.file, but I > > still have problems, > > I attached the images which show my atals and annotation file loaded > > into tkmedit and tksurfer, the surface is > > broken. > > > > Could you tell me what I need to do? > > > > Thanks a lot! > > Guang > > > > > > > Date: Wed, 16 Dec 2009 18:05:03 -0500 > > > From: greve(a)nmr.mgh.harvard.edu > > > To: freesurfer_zg(a)hotmail.com > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > Load it again in tkmedit to make sure you have the color table right, > > > then re-run you mris_seg2annot command with your color table. > > > > > > doug > > > > > > Guang Zeng wrote: > > > > Hello, Doug, > > > > > > > > I am transfering my color lookup table to FreeSurfer ColorLUT now. It > > > > may need a little while. > > > > I load the a.anat.mgz using tkmedit and FreeSurfer lookup table, > > > > although the label and the colors looks a little bit > > > > strange, but all the other things look fine to me such as the > > > > segmentation results are registered pretty well. > > > > > > > > Could you tell me what I need to do next, once my color lookup table > > > > is ready, > > > > > > > > Thanks! > > > > Guang > > > > > > > > > Date: Wed, 16 Dec 2009 17:39:07 -0500 > > > > > From: greve(a)nmr.mgh.harvard.edu > > > > > To: freesurfer_zg(a)hotmail.com > > > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > > > > > First, work in the volume instead of the surface because the > > surface is > > > > > too hard to determine what is going on. Convert a.nii to the > > anatomical > > > > > space with > > > > > > > > > > mri_vol2vol --mov a.nii --reg > > > > > $FREESURFER_HOME/subjects/sub1/compare/register_raw.dat --interp > > > > > nearest --fstarg \ > > > > > --o $FREESURFER_HOME/subjects/sub1/mri/a.anat.mgz > > > > > > > > > > Then look at the output in tkmedit: > > > > > > > > > > tkmedit sub1 orig.mgz -surfs -seg a.anat.mgz YOURLUT > > > > > > > > > > where YOURLUT is a color lookup table for your segmentation > > (model it > > > > > using FreeSurferColotLUT.txt). > > > > > > > > > > let me know if that looks ok > > > > > > > > > > doug > > > > > > > > > > Guang Zeng wrote: > > > > > > Hello, Doug, > > > > > > > > > > > > Thanks a lot for your quick reply, I removed that "ico 7", now > > it is: > > > > > > > > > > > > mri_vol2surf --src a.nii --src_type nifti --srcreg > > > > > > $FREESURFER_HOME/subjects/sub1/compare/register_raw.dat --hemi > > rh --o > > > > > > ./atlas-rh.mgz --out_type mgh --float2int round --interp nearest > > > > > > > > > > > > and I rerun the two commands, it finished without problems. > > > > > > > > > > > > But I tried to take a look at this annotation file, I load the > > volume > > > > > > use tksurfer, then import my myatalas.annot, a multiple-line > > warning > > > > > > is showed as > > > > > > : Warning: vertex 132436 with annotation ffffffff - out of range! > > > > > > > > > > > > Could you give me some suggestions to fix it? > > > > > > > > > > > > The original input file I loaded into tksurfer has been converted > > > > into > > > > > > the anatomical space, and my first-command line input a.nii > > has been > > > > > > registered to it using tksurfer. > > > > > > > > > > > > Thanks a lot! > > > > > > Gaung > > > > > > > > > > > > > Date: Wed, 16 Dec 2009 17:12:50 -0500 > > > > > > > From: greve(a)nmr.mgh.harvard.edu > > > > > > > To: freesurfer_zg(a)hotmail.com > > > > > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > > > > > > > > > Sample it to the native subject's space with mri_vol2surf (not > > > > to ico > > > > > > > 7). Is the input file a.nii already in the anatomical space > > (ie, > > > > 256^3, > > > > > > > 1mm^3)? If not, make sure that your registration matrix is > > correct > > > > > > using > > > > > > > tkregister2. > > > > > > > > > > > > > > doug > > > > > > > > > > > > > > Guang Zeng wrote: > > > > > > > > Hello, Doug, > > > > > > > > > > > > > > > > Thanks a lot for your help, I am following your > > instruction now, > > > > > > > > > > > > > > > > First Step: mri_vol2surf > > > > > > > > my command line is > > > > > > > > mri_vol2surf --src a.nii --src_type nifti --srcreg > > > > > > > > $FREESURFER_HOME/subjects/sub1/compare/register_raw.dat > > --hemi > > > > rh --o > > > > > > > > ./atlas-rh.mgz --out_type mgh --float2int round > > --trgsubject ico > > > > > > > > --icoorder 7 --interp nearest > > > > > > > > > > > > > > > > Second step: mris_seg2annot > > > > > > > > my command line is > > > > > > > > mris_seg2annot --seg atlas-rh.mgz --ctab > > > > > > > > $FREESURFER_HOME/FreeSurferColorLUT.txt --s sub1 --h rh --o > > > > > > > > myatalas.annot > > > > > > > > > > > > > > > > But I got error like, > > > > > > > > ERROR: dimension mismatch. Surface has 132464 vertices, seg > > > > has 163842 > > > > > > > > Make sure the surface segmentation matches the subject and > > hemi > > > > > > > > > > > > > > > > Could you give me some suggestions to fix it? > > > > > > > > > > > > > > > > Thanks! > > > > > > > > Guang > > > > > > > > > > > > > > > > > > > > > > > > > Date: Wed, 16 Dec 2009 13:12:59 -0500 > > > > > > > > > From: greve(a)nmr.mgh.harvard.edu > > > > > > > > > To: freesurfer_zg(a)hotmail.com > > > > > > > > > CC: freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > > Subject: Re: [Freesurfer] a question about mris_ca_train > > > > > > > > > > > > > > > > > > You can use mri_vol2surf with the --interp nearest > > option to > > > > sample > > > > > > > > your > > > > > > > > > volume segmentations onto the surface. You can then use > > > > > > mris_seg2annot > > > > > > > > > to convert this segmentation directly to an annotation, > > then use > > > > > > > > > mri_annotation2label to convert the annotation into a > > set of > > > > labels. > > > > > > > > > Nothing here guarantees that labels will be connected or > > > > > > contiguous nor > > > > > > > > > is it sure that all vertices on the surface will be labeled. > > > > > > > > > > > > > > > > > > doug > > > > > > > > > > > > > > > > > > Guang Zeng wrote: > > > > > > > > > > Hi, there, > > > > > > > > > > > > > > > > > > > > Recently, I sent sseveral emails to you to ask same > > kind of > > > > > > question > > > > > > > > > > about building our own template and atlas. > > > > > > > > > > Thanks a lot for your quick reply, they helps me a lot. > > > > > > > > > > > > > > > > > > > > Currently, I still have a question about building our own > > > > > > atlas using > > > > > > > > > > mris_ca_train, sorry to bother you again. > > > > > > > > > > > > > > > > > > > > We have a surface labeling atlas in our lab, we'd like to > > > > use this > > > > > > > > > > atlas instead of using FS's > > desikan_killiany.2007-06-20gcs. > > > > > > > > > > It is kind of difficult for us to load every subject > > in our > > > > > > training > > > > > > > > > > set to tksurfer, and manually label each ROI based on our > > > > ATLAS. > > > > > > > > > > > > > > > > > > > > What we try to do is: > > > > > > > > > > 1. Send each subject in the training set to our > > toolbox which > > > > > > will > > > > > > > > use > > > > > > > > > > our atlas to do surface labeling. For each subject it will > > > > > > output a > > > > > > > > > > file just like > > > > > > > > > > wmparc.mgz in FS, but it is NIfTI file. > > > > > > > > > > > > > > > > > > > > 2. Send each subject to FS pipeline to get the > > ?h.sphere.reg, > > > > > > ?h.sulc > > > > > > > > > > files. > > > > > > > > > > > > > > > > > > > > 3. Find a method to get my ?h. mylabels. annot files, > > and use > > > > > > > > > > mris_ca_train to build a new atlas. > > > > > > > > > > > > > > > > > > > > First of all, do you think what I try to do is reasonable? > > > > > > > > > > > > > > > > > > > > If yes, I know I need to get the FS .label files for each > > > > ROI, > > > > > > then I > > > > > > > > > > can call mris_label2annot to get ?h. mylabels. annot > > files. > > > > > > > > > > > > > > > > > > > > But how can I get the FS .label files for each ROI > > from our > > > > > > toolbox > > > > > > > > > > output ROI labeled NIfTI file? > > > > > > > > > > > > > > > > > > > > These qurstions trouble me for a long time, your help are > > > > really > > > > > > > > > > appreciate. > > > > > > > > > > > > > > > > > > > > Thanks a lot! > > > > > > > > > > Guang > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > Your E-mail and More On-the-Go. Get Windows Live > > Hotmail Free. > > > > > > > > Sign up > > > > > > > > > > now. <http://clk.atdmt.com/GBL/go/171222985/direct/01/> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > > 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: > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > Freesurfer mailing list > > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. > > > > > > Sign up > > > > > > > > now. <http://clk.atdmt.com/GBL/go/171222985/direct/01/> > > > > > > > > > > > > > > -- > > > > > > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. > > > > Sign > > > > > > up now. <http://clk.atdmt.com/GBL/go/177141664/direct/01/> > > > > > > > > > > -- > > > > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > Hotmail: Free, trusted and rich email service. Get it now. > > > > <http://clk.atdmt.com/GBL/go/171222984/direct/01/> > > > > > > -- > > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > ------------------------------------------------------------------------ > > Hotmail: Free, trusted and rich email service. Get it now. > > <http://clk.atdmt.com/GBL/go/171222984/direct/01/> > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/

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Freesurfer December 2009