Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

images use different protocols
by Wang, Xin 16 Aug '07

16 Aug '07

Hello, Group I have two set of images acquired with different imaging protocols (e.g., TRs and bandwidth are different). Can I poll them together for the analysis? I saw in the email list that some groups reported problems in generating the average of images with different TR for the group analysis. I do not seem have problem to make average include all the images. But is the result acceptable if the images acquired with multiple protocols? Thank you

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procedural question about FDR correction
by Dara Manoach 16 Aug '07

16 Aug '07

Hi, FDR correction for multiple comparisons gives you different p-values for the left and right hemispheres. It seems really weird to report in a paper: a) that you've corrected for the right and left hemispheres separately and b) that the p-value that gave rise to a corrected probability of .05 was different for each. How do people deal with this issue? Take the most stringent p-value and use it for both hemispheres? Just report that FDR adjusted the p- value to .05? Also, correcting for right and left hemispheres separately assumes that they are independent observations. Unless you're studying callosotomy patients (and maybe even if you are) this doesn't seem justified. Are we supposed to be adjusting p-values accordingly? Thanks, Dara Dara S. Manoach, Ph.D. Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th Street, Room 2608 Charlestown, MA 02129 email: dara(a)nmr.mgh.harvard.edu phone: 617-724-6148 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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mri_surf2vol
by Leila BH 16 Aug '07

16 Aug '07

Hello, I need to convert the white matte surface to a volume :binary volume with 1 in white matter and 0 outside. I am using the mri_surf2vol command (on both hemisphere), and fill it using matlab. Do you know if it is possible to obtain the volume from the surface already filled ? Thanks a lot. Here is the command I use : Mri_surf2vol --mkmask --hemi lh --template /my_image.img --volregidentity mysubject --outvol outputvol_lh.img

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Assertion failed at line 827 in file templates/CachedArray.cc
by Richard Frye 15 Aug '07

15 Aug '07

While running freesurfer I obtain the following error message Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)ERROR: nu_correct The mri looks okay. I cannot find anything in the wiki Any ideas appreciated. -- Best Wishes, Richard E. Frye, M.D., Ph.D., F.A.A.P. Assistant Professor of Pediatrics and Neurology University of Texas Medical School at Houston 7000 Fannin -- UCT 2478 Houston, TX 77030 Office: 713-500-3245 e-mail: richard.frye(a)gmail.com

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qdec / qcache
by Claus Reinsberger 14 Aug '07

14 Aug '07

Hi everybody, I tried to run the qdec-tool in the dev-env, but experienced some problems with my last subject. This is the environment, I'm working in: FREESURFER_HOME: /usr/local/freesurfer/dev Build stamp: freesurfer-Linux-centos4-dev-20070811 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp i686 NMR Center info (/space/freesurfer exists): machine: tkmeg SUBJECTS_DIR: /space/megraid/83/MEG-MRI/seder/freesurfer/ PWD: /space/megraid/83/MEG-MRI/seder/freesurfer ... and here's the error I get when I start the group analysis in qdec, subj nmr00199 is the one I added (after I ran -qcache): ERROR: dimension mismatch between /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nm r00188_a/surf/lh.thickness.fwhm10.fsaverage.mgh and /autofs/space/megraid_083/MEG-MRI/s eder/freesurfer/nmr00199/surf/lh.thickness.fwhm10.fsaverage.mgh Error in Analyze: command failed: mri_concat /autofs/space/megraid_083/MEG-MRI/seder/fr eesurfer/nmr00188_a/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/ME G-MRI/seder/freesurfer/nmr00172_a/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/ megraid_083/MEG-MRI/seder/freesurfer/nmr00035/surf/ lh.thickness.fwhm10.fsaverage.mgh /a utofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00039_a/surf/ lh.thickness.fwhm10.fs average.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00046/surf/ lh.thickne ss.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00127/sur f/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/ nmr00156/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder /freesurfer/nmr00158/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/M EG-MRI/seder/freesurfer/nmr00159/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/m egraid_083/MEG-MRI/seder/freesurfer/nmr00180_a/surf/ lh.thickness.fwhm10.fsaverage.mgh / autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00189_a/surf/ lh.thickness.fwhm10.f saverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00034/surf/ lh.thickn ess.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00031_a/ surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurf er/nmr00070/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/se der/freesurfer/nmr00098/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_08 3/MEG-MRI/seder/freesurfer/nmr00013/surf/ lh.thickness.fwhm10.fsaverage.mgh /autofs/spac e/megraid_083/MEG-MRI/seder/freesurfer/nmr00182_a/surf/ lh.thickness.fwhm10.fsaverage.mg h /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00052/surf/ lh.thickness.fwhm10. fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00123/surf/ lh.thick ness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00076/s urf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfe r/nmr00183_a/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/s eder/freesurfer/nmr00184_a/surf/lh.thickness.fwhm10.fsaverage.mgh /autofs/space/megraid _083/MEG-MRI/seder/freesurfer/nmr00181_a/surf/ lh.thickness.fwhm10.fsaverage.mgh /autofs /space/megraid_083/MEG-MRI/seder/freesurfer/nmr00068/surf/ lh.thickness.fwhm10.fsaverage .mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00073/surf/ lh.thickness.fwhm 10.fsaverage.mgh /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/nmr00199/surf/lh.th ickness.fwhm10.fsaverage.mgh --o /autofs/space/megraid_083/MEG-MRI/seder/freesurfer/qde c/Untitled/y.mgh Could this be due to the dev-env of the qcache-command (the log says everything went fine)? Autorecon-3 also seems to have run fine in this patient. Thanks a lot for your help, Claus

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Wiki Request
by Daniel G. Wakeman 14 Aug '07

14 Aug '07

Hello, I would like to request that the Freesurfer wiki be added to the interwiki map (see link below). This would streamline linking for individual lab's wikis to pages on the freesurfer wiki of commands (for example). Dan http://meta.wikimedia.org/wiki/Interwiki_map

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problem with diff-flirt
by Marcus Belke 14 Aug '07

14 Aug '07

Hi we are currently working on the DTI data and we are trying to get the mc-step running using diff-flirt. it does not work, although the unpacking and the dtrecon seem to work fine. I have attached the log-file and copied the error message at the bottom. Can anyone help? Thanks a lot! Best regards, Marcus -------- ERROR MESSAGE-------- ... ... Registering volume 1 flirt -in ./tmp/diff-flirt-8311/f-001.img -ref ./tmp/diff-flirt-8311/f-000.img -out ./tmp/diff-flirt-8311/f-001.img -omat ./tmp/diff2diff-001.mat -verbose 3 -dof 12 -searchrx -15 15 -searchry -15 15 -searchrz -15 15 -cost mutualinfo -searchcost mutualinfo -bins 256 WARNING!!!! Multiple image files detected: ./tmp/diff-flirt-8311/f-000.nii.gz ./tmp/diff-flirt-8311/f-000.img ./tmp/diff-flirt-8311/f-000.hdr STOPPING PROGRAM ERROR: flirt failed with status 1 ___________________________________________________________ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html

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(no subject)
by Troy Mcan 13 Aug '07

13 Aug '07

Hi,I am wondering if part of this process can be turned into a script:I am forming ROIs in freesurfer using tksurfer and a long list of talairach coordinates. Here is my process:1) I use the "select_talairach_point x y z" function, then I click the point that is highlighted on the brain from the command, and note the vertex point.2) Once all of the talairach coordinates have been entered in with this method, the brain surface is filled with a bunch of "dots." I manually scan the brain and note which points form the boundary of the region.3) Using the command "mark_vertex # 1", I mark the boundary vertices of this "spotted region". Once these are marked, I use the command "path_new_path_from_marked_vertices".4) This forms a path around the boundary vertices. I use the "make closed path" button to close this boundary, then fill it in and save it as a label.I am looking for a way to keep the list of talairach points saved in a file. I have upwards of 200 points that I need to type in continually for each subject, and I would like to bring them into tksurfer in one step (scripted, perhaps?) and have them marked on the brain surface, so I can manually proceed to find the boundary vertices, etc.etc. I am not too concerned with scripting anything past step 1.I would greatly appreciate any help! Thanks! _________________________________________________________________ Messenger Café — open for fun 24/7. Hot games, cool activities served daily. Visit now. http://cafemessenger.com?ocid=TXT_TAGLM_AugWLtagline

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tkmedit dev version
by Chuan.Chih.Yang＠rwth-aachen.de 13 Aug '07

13 Aug '07

Dear list, I have a problem to open tkmedit under dev version, here is the message I got. [MPIB7193-R-52c:~] jackie% tkmedit X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 129 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 15 Current serial number in output stream: 15 [MPIB7193-R-52c:~] jackie% Thank you for the help jackie

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Fixing defects on inflated brain
by Nandita Shetty 13 Aug '07

13 Aug '07

Hi, I ran the first two steps of recon-all and it completed with no errors. I took a look at the inflated brain and it (the shape) does not seem right. There are some dimples, bumps etc which I know how to fix but I cant seem to figure out what is causing the deformed shape. If you could give me a pointer or two regarding this, it would be very helpful. Thanks in advance ! :) Env : nmrstdenv Machine name : Marvin SUBJECTS_DIR : /autofs/space/marvin_001/users/MRI/WMA/ SUBJECT : 002201

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