Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30085 discussions

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

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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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recon-all error (sample tutorial data)
by Hui J Yu 17 Dec '09

17 Dec '09

Dear freesurfer users, I have recently downloaded freesurfer (virtualbox verion) and started testing using the sample data bert. I got the following error (I also tried on my data and the same error occured). Any suggestions? ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...46 iterations mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/bert/mri/T1.mgz',frame -1, errno 12 mri_strip_skull: done peeling brain Brain Size = 1793357 voxels, voxel volume = 1.000 mm3 = 1793357 mmm3 = 1793.357 cm3 mri_watershed Error: read failed Linux freesurfer-virtual 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Thu Dec 17 17:20:18 EST 2009 Thank you. Hui Jing Yu

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Announcement: Colin dataset download
by Krish Subramaniam 17 Dec '09

17 Dec '09

Please find the download information in the following wiki-page -- http://surfer.nmr.mgh.harvard.edu/fswiki/Colin27 Thanks Krish

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lGI error (error with class.m function)
by Frédéric Andersson 17 Dec '09

17 Dec '09

Hi, I've got some troubles computing the lGI. It seems to be a trouble related to the class.m and strel.m matlab functions. Does anyone meet such problem? Thanks Frederic gray.local:andersson 11:50am [12] recon-all -s MNI_SINGLESUBJ -localGI -no-isrunning INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /usr/remote/Darwin/freesurfer/freesurfer450/ subjects Actual FREESURFER_HOME /usr/remote/Darwin/freesurfer/freesurfer450 -rw-rw-r-- 1 andersson flat 750913 Dec 17 09:29 /usr/remote/Darwin/ freesurfer/freesurfer450/subjects/MNI_SINGLESUBJ/scripts/recon-all.log Darwin gray.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/remote/Darwin/freesurfer/freesurfer450 Previous: /usr/remote/Darwin/freesurfer/freesurfer410 /usr/remote/Darwin/freesurfer/freesurfer450/subjects/MNI_SINGLESUBJ/surf #-------------------------------------------- #@# Local Gyrification Index lh Thu Dec 17 11:50:50 CET 2009 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf /usr/remote/Darwin/freesurfer/freesurfer450/subjects/ MNI_SINGLESUBJ/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /usr/remote/Darwin/freesurfer/freesurfer450/subjects/ MNI_SINGLESUBJ/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /usr/remote/Darwin/freesurfer/freesurfer450/ subjects/MNI_SINGLESUBJ/surf/tmp-mris_compute_lgi-lh.pial/ lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /usr/remote/Darwin/freesurfer/freesurfer450/ subjects/MNI_SINGLESUBJ/surf/tmp-mris_compute_lgi-lh.pial/ lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/usr/remote/Darwin/freesurfer/freesurfer450/ subjects/MNI_SINGLESUBJ/surf/tmp-mris_compute_lgi-lh.pial/ lh.pial.filled.mgz',15,'/usr/remote/Darwin/freesurfer/freesurfer450/ subjects/MNI_SINGLESUBJ/surf/tmp-mris_compute_lgi-lh.pial/lh.pial- outer'); exit ================= Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.5.0.338 (R2007b) August 9, 2007 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> reading filled volume... interactive shell interactive shell closing volume... ??? Error using ==> class The CLASS function must be called from a class constructor. Error in ==> strel>MakeArbitraryStrel at 188 se = class(se, 'strel'); Error in ==> strel at 122 se = MakeArbitraryStrel(params{:}); Error in ==> strel>MakeBallStrel at 530 se.decomposition = strel(nhood,height); Error in ==> strel at 141 se = MakeBallStrel(params{:}); Error in ==> make_outer_surface at 41 se=strel('ball',se_diameter,se_diameter); >> Frédéric ANDERSSON, PhD Ingénieur de Recherche INSERM / IFR 135 - Imagerie fonctionnelle Faculté de Médecine 10 Blvd Tonnellé Bat. Vialle - 2ème étage - Bureau 205 BP 3223 - 37032 TOURS cedex - FRANCE Tél : +33 (0) 2 47 36 61 37 / Fax: +33 (0) 2 47 36 62 07

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fsaverage to mni152
by Yigal Agam 17 Dec '09

17 Dec '09

Hi, What's the best way to convert an fsaverage volume into an MNI152 volume that can be viewed on top of a standard brain (MNI152_T1_2mm_brain.nii.gz) in fslview? Thanks, Yigal

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Graphics Card Question
by Sam Evans 17 Dec '09

17 Dec '09

Dear all I am new to FreeSurfer and would apprechiate some advice. I am about to purchase a graphics card specifically to use Free Surfer due to the nature of the desk top I have I am restricted in my choice of options. I have been recommended the ATI Radeon HD3450 and HD3470: http://accessories.euro.dell.com/sna/productdetail.aspx?c=uk&l=en&s=bsd&cs=… http://accessories.euro.dell.com/sna/productdetail.aspx?c=uk&l=en&s=bsd&cs=… Will these be up to spec for use with Free Surfer? I am planning to use these with Ubuntu. Is there anything I should know about before I take the plunge and buy them? Thanks in advance for your help Sam

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error with libtix8.1.8.4.so
by Sungeun Kim 16 Dec '09

16 Dec '09

Hello, Thank you for all help in advance. Recently, I installed the FreeSurfer ver.4.5.0 (centos4_x86_64-stable-pub-v4.5.0) on my mint 8 linux (x86_64). When I tried to run a command (recon-all) on my terminal, I didn't see any problem and all help messages were returned. But I tried to run tkmedit and tksurfer, I got an error message: "tkmedit.bin: error while loading shared libraries: libtix8.1.8.4.so: cannot open shared object file: No such file or directory" To check the dependency of tkmedit, I ran "which tkmedit' and "ldd `which tkmedit`" on a terminal. Two commands returned ..>which tkmedit /usr/local/freesurfer/bin/tkmedit ..> ldd `which tkmedit` not a dynamic executable Here is my LD_LIBRARY_PATH: ..>echo $LD_LIBRARY_PATH /lib:/usr/lib:/lib32:/usr/lib32:/usr/local/lib64:/usr/local/lib I am using freesurfer often for my research. So, any help or suggestion to resolve this issue would be really helpful to me. -- Sungeun Kim

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