Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Number of orig volumes
by pikase＠tin.it 28 May '10

28 May '10

Hi everyone, maybe this is a trivial question but I didn't find an answer in the archives, so I'll post it anyway. I've noticed in articles on cortical thickness using freesurfer that the number of initial T1 volumes (orig) is quite variable, ranging from 1 to 3 or 4. We are planning to evaluate the cortical thickness for a large sample (30/40 subjects), and we have 1 volume for each subject (3T, 200 slices. 1mm). I was wondering whether using a single volume could affect the results. However, I've already processed 15 subjects and the results look nearly perfect to me. Best regards Laura

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Mask with different contrasts in tksurfer
by caspari＠clipper.ens.fr 28 May '10

28 May '10

HI! Is it possible do generate masks out of two (or more) different overlays ( name.w file)/ contrasts, to then in the end display the overlapping acitvation in a new overlay? The aim would be to get/create ROIs/Labels, which are already masked for plotting their timecourses. How could this work for the single subject? I hope someone has an idea??? I'm already a bit desesperate.. Thanks a lot- Natlaie

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using mris_make_template
by Danny Kim 27 May '10

27 May '10

hello all, first time poster and apologize in advance if this question has been addressed previously.. can someone provide an example script of how to use the mris_make_template command? I am mainly confused about what the input should be and what the output should look like. I've tried: mris_make_template lh sphere.reg EP068 ./desktop/FS_EP068_TEMPLATE/lh_test.tif and it produced a .tif file at the output location but this doesn't look at all like the .tif files located in /Freesurfer/average folders. Any help would be appreciated. Thanks!! Danny Kim Brainmapping centre BC Children's Hospital 4480 Oak Street Vancouver BC Canada

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mri_motion_correct.fsl buglet
by Sebastian Moeller 27 May '10

27 May '10

Dear Freesurfers, I just tried to use mri_motion_correct.fsl with the -tmpdir and -nocleanup options. Since I currently average around 10 to 16 mprage volumes per subject (NHPs) I want to look at the variance in addition to the average. And it seemed simplest to just keep the co-registered volumes in the tmpdir around and calculate the variance from those. But, it turns out that the -nocleanup does not work (nor does the implied -nocleanup that is set from -tmpdir (set CleanUp = 0)). The problem seems to be fixable by changing: cleanup: if($#CleanUp > 0) then foreach f ($CleanUpList) rm -f $f end endif rm -r $tmpdir goto cleanup_return; to: cleanup: if($#CleanUp > 0) then if (${CleanUp} == 1) then echo "cleaning up..." foreach f ($CleanUpList) rm -f $f end endif endif if (${CleanUp} == 1) then rm -r $tmpdir endif goto cleanup_return; or even simpler: goto cleanup; cleanup_return: to: if (${CleanUp} == 1) then goto cleanup; cleanup_return: endif it would be great if this could be included into the next version. (It would certainly make my life easier :)) Best Regards Sebastian

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aparc+aseg is all left cerebral white matter
by Elias Kersten 27 May '10

27 May '10

Hi, I am trying to run a subject through the entire recon-all pipeline. However, I noticed the second to last step, "-wmparc", was taking a very long time (days). Looking over the data, the aparc+aseg.mgz file is almost all labeled as "Left-Cerebral-White-Matter", including the background. Also, the lh.ribbon.mgz file appears like a series of speckles, while the rh.ribbon.mgz file looks normal. I'm not sure where this problem is originating from or what my next steps should be. Any suggestions? Thanks, Elias

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corpus callosum volumetry of some sagital slices only...
by Gonzalo Rojas 27 May '10

27 May '10

Hi: How can I get the volumetry of the corpus callosum in only some sagital slices ?... For example, 5 slices to the left and 5 to the right the medial line ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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fixing cortical parcellation
by Esther Walton 27 May '10

27 May '10

Hi, I just came across a cortical parcellation issues (see attachment), which I got when running tksurfer M02111314 rh pial -annot aparc There is a small-ish orange blob (belonging to the parstriangularis) seeming to be misplaced slightly to the left onto the parsopercularis and I was wondering what ways there are to fix it. I look up the freesurfer wiki, but couldn't really find anything about this. I mean this wouldn't work with control points or the like, right? Thanks for your help, Esther _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:…

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Cortical parcellation-related
by Bauer, Andrew J 27 May '10

27 May '10

Hi, I know how to create annotation files via the "mris_ca_label" command. However, I'm curious as to HOW the following file is created (which is found in the "mri" folder of a subject), and WHEN it was created: aparc.a2009s+aseg.mgz I recently installed FS and I'm working only with the sample "bert" folder. Thus there are a lot of files pre-created, and I'm wondering how some were created. I'd like to end up with an "aparc.a2009s+aseg.mgz" file for each subject, but I don't know how to go from cortical parcellation annotation files to a volume form with the parcellation mapped onto it. Just to let you know, ultimately I'd like to convert the volume with cortical parcellation into an AFNI BRIK. Apologies in advance if my question seems confusing. Please advise! And please let me know if you need any further information. Thanks. -- AJB

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color wheel woes
by Chris Said 27 May '10

27 May '10

Hi, I know that there have been questions about the color wheel in the past, and that future versions of tksurfer will resolve some of the issues. But in the meantime, I was wondering if I could get some help with the existing version: (1) Does anybody have access to good images of the color wheel or RYGB wheel, for use in displaying eccentricity and polar angle maps? Or alternatively, if someone just has a list of the RGB values for these wheels, I could make the images of the wheels myself (and can give them to anyone else who might want them). (2) In the Configure Overlay panel, changing the the offset has an effect on non-complex data, but it has no effect on complex data. Does anybody know how to change the offset for complex data? Thanks very much for your help. Chris

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mac installation problems
by Ed Vessel 26 May '10

26 May '10

Hi folks - I just installed Freesurfer on my Mac (OSX 10.5.8, quad-core intel xeon). The environment variables appear to be set up properly. >source ~/.tcshrc -------- freesurfer-Darwin-leopard-ppc-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /CBI/bin/fsldir However, when I try to run some of the programs, I encounter errors: >tkmedit bert orig.mgz X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 16 Current serial number in output stream: 16 [nothing loads] >qdec dyld: Library not loaded: /sw/lib/libtiff.3.dylib Referenced from: /Applications/freesurfer/lib/vtk/lib/ libvtkVolumeRendering.5.0.dylib Reason: image not found Trace/BPT trap [nothing loads] >tksurfer bert rh pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Network/Servers/TESLA.CBI.FAS.NYU.EDU/Volumes/data1/Home/ vessel surfer: Reading header info from /Applications/freesurfer/subjects/ bert/mri/T1.mgz surfer: vertices=131860, faces=263716 WARNING: No colortable found! surfer: single buffered window surfer: tkoInitWindow(bert) Received X error! Error code : 1 Request code : 128 Minor code : 1 Error text : 'BadRequest (invalid request code or no such operation)' surfer: using interface /Applications/freesurfer/lib/tcl/tksurfer.tcl [does continue to load properly] So, it looks like perhaps I'm having some issues with X, and perhaps the tk libraries. Do you have any suggestions on what I might need to do? X version: XQuartz 2.1.6 (xorg-server 1.4.2-apple33) thanks, Ed -- Ed Vessel Center for Brain Imaging New York University ed.vessel(a)nyu.edu 4 Washington Place, Rm. 156 New York, NY 10003 http://www.cns.nyu.edu/~vessel (212) 998-8217

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