Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

Differing OS X version and recon-all
by Chiu, Bryan (PHTH) 22 May '14

22 May '14

Hi, Wanted to check in about Mac OS X and any effects on recon-all that I may not be aware of. A while back the Mac was updated to 10.9.2 from some other version of 10.x.x. I ran half of my recon-all on 10.x.x, and am running my 2nd half on 10.9.2. The update was due to some IT person thinking the older version had security flaws. Will I need to rerun all of my subjects on 10.9.2, or has there been no reported differences between these two versions? Thanks, - Bryan

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mri_vol2vol memory error
by Ben Mooneyham 22 May '14

22 May '14

Hello all, I am doing pre-processing for resting-state fMRI volumes, but I have encountered an error and am unsure of how to correct it: I have previously determined the nonlinear warping transformations from my subjects' anatomical (T1) space to the 2mm MNI template using ANTs. At the end of my pre-processing pipeline, I am trying to transform my subjects' functional volumes (206 TRs of 2sec) into this MNI space by 1) transforming the functional volumes into subject T1 space using mri_vol2vol, and 2) applying the nonlinear warp (from ANTs) to the volumes in subject-T1 space to ultimately have my subjects' functional data in MNI space. However, I am getting an error while running mri_vol2vol, where it "cannot allocate region." I gather from looking around online that this is a memory issue, but I am not sure how to fix it. Thoughts? It is crucial that I be able to translate my functional data into common MNI space before performing second-level analyses... I do not encounter this issue when performing this transformation on functional connectivity maps (where I take an ROI defined in MNI space, transform it into T1, and then subject-EPI space, calculate the FC with the rest of the brain, and then invert the process by transforming back into T1, and finally MNI space). How can I get this to work with a larger file? Thank you in advance for your help, Ben Mooneyham -- Graduate Student UCSB - Department of Psychological & Brain Sciences Building 429 Room 102 (210) 912-6076 bwmooneyham(a)gmail.com

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installation recon-all
by Ashley Rose 22 May '14

22 May '14

Hi Freesurfers, I've downloaded and installed Freesurfer on in VirtualBox running Ubuntu 12.04 (on a Windows 7 host machine). In my shell, though, it's installed with CentOS4 (see below) I've been working through the page on testing the installation. Everything works nicely, until I get to the recon-all commands. When I try having it just run the -autorecon1 stage on its own, I get this error: -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni arose@HarryCallahan:/usr/local/freesurfer/subjects/buckner_data/tutorial_subjs$ recon-all -s bert -autorecon1 WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer rm: cannot remove `/usr/local/freesurfer/subjects/bert/scripts/recon-all.cmd': Permission denied mv: cannot move `/usr/local/freesurfer/subjects/bert/scripts/recon-all.env' to `/usr/local/freesurfer/subjects/bert/scripts/recon-all.env.bak': Permission denied -rw-rw-rw- 1 root root 805935 May 21 16:53 /usr/local/freesurfer/subjects/bert/scripts/recon-all.log Linux HarryCallahan 3.11.0-20-generic #35~precise1-Ubuntu SMP Fri May 2 21:32:55 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux rm: cannot remove `/usr/local/freesurfer/subjects/bert/scripts/recon-all.done': Permission denied /usr/local/freesurfer/subjects/bert/scripts/IsRunning.lh+rh: Permission denied. arose@HarryCallahan:/usr/local/freesurfer/subjects/buckner_data/tutorial_subjs$ Is there something simple that I do so that the files it creates are automatically allowed to be moved/removed etc? The sudo command doesn't help, unfortunately. Thanks in advance, Ashley

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Classifying thickness question
by pfotiad＠nmr.mgh.harvard.edu 22 May '14

22 May '14

Hi Bruce, I had a few questions concerning the mris_classify_thickness algorithm that you wrote: 1) Are there any other options (i.e. other flags) that can be specified in the mris_classify_thickness -o <output subject> [options] <hemi> <surf> <curv> <c1_subject1> <c1_subject2>... : <c2_subject1> <c2_subject2>... commandline? Because in the description of the command there is nothing reported under the "valid options are:" I believe I saw some other options reported in the code of the specific function, but I wasn't sure whether they could be used. 2) Are the two classes defined as two different groups of subjects such as male/female or healthy/disease? 3) I ran the command on 4 subjects (class1: 2 diseased subj, class2: 2 healthy subjs) and the result was 2 data files with 202 pairs of cortical thickness values each. However, I'm not really sure what those values represent. Are they vertex-wise thickness values that correlate somehow between <c1_subject1> <c1_subject2>, and <c2_subject1> <c2_subject2>, respectively, or are they clustered-wise thickness values? 4) Are there any other outputs besides those two data files that the command can come up with? Thanks in advance for all your help! Panos

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Re: [Freesurfer] mri_vol2vol memory error
by Douglas N Greve 22 May '14

22 May '14

Hi Ben, please post questions to the list and not to us personally. Thanks! I do not have an alternative. I think you are using Thomas Yeo's stream which we are not supporting. He just uses binaries from FS. doug On 05/22/2014 12:16 PM, Ben Mooneyham wrote: > Hi Douglas, > > Thank you for your response. Would you perhaps be able to suggest an > alternative approach that may work for my situation? > > - Ben M > > -- > Graduate Student > UCSB - Department of Psychological & Brain Sciences > Building 429 Room 102 > (210) 912-6076 > bwmooneyham(a)gmail.com <mailto:bwmooneyham@gmail.com> -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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wm and ctx labels - mri_aparc2aseg
by Andrea Tateo 22 May '14

22 May '14

Hi FreeSurfer expert, after that I have used the command "recon-all" I would like to obtain wm-lh and wm-rh information ( for example wm-lh-bankssts,wm-lh-caudalanteriorcingulate,wm-lh-caudalmiddlefrontal, ...). I have read that mri_aparc2aseg command can help me, but when I use it I have two problems: 1) When I use the command mri_aparc2aseg --s subject I obtain as output the image "aparc+aseg.mgz" which contains information only about cortical label. 2) When I use the command mri_aparc2aseg --s subject --a.2005 I get the following message: ERROR: Option --a2005 unknown Can you help me? Moreover, the recon-all output in directory /mri is: aparc.a2009s+aseg.mgz, aparc+aseg.mgz, aseg.auto.mgz, aseg.auto_noCCseg.label_intensities.txt , aseg.auto_noCCseg.mgz aseg.mgz, brain.finalsurfs.mgz, brainmask.auto.mgz, brainmask.mgz, brain.mgz, ctrl_pts.mgz, filled.mgz, lh.ribbon.mgz, mri_nu_correct.mni.log, norm.mgz, nu.mgz, nu_noneck.mgz, orig, orig.mgz, rawavg.mgz, rh.ribbon.mgz, ribbon.mgz, segment.dat , T1.mgz, talairach.label_intensities.txt , talairach.log, talairach_with_skull.log, transforms, wm.asegedit.mgz, wm.mgz, wmparc.mgz , wm.seg.mgz Do you think that the searched information is here? Thanks for your help. Best regards, Andrea

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missing temporal lobes
by Daly, Eileen 22 May '14

22 May '14

Hello all, We are having trouble with the output after running recon-all -all -subjid subjectx on our scans. Registrations and skull striping look okay, but the white matter and pial surface segmentations leave outportions of the anterior temporal lobe. After adding control points to the left temporal lobe, we then ran recon-all -autorecon2 -cp -autorecon3 -subjid subjects. This made the the left lobe look better, but then we spotted new missing bits on the right side anterior temporal lobe. Any ideas on dealing with these missing temporal lobe issues? Thanks, Eileen Daly

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creating custom color table & annotation file
by Maria Jalbrzikowski 21 May '14

21 May '14

Dear Freesurfer experts, I would like to get your help. I extracted cortical thickness values from each vertex from each of my individual subjects (example: path/subject_id/surf/lh.thickness.fsaverage.mgh). I then ran a covariance analysis over the whole group and identified "modules" or groups of vertices that covary together. The modules are given the names of colors. I end up with a module (color) assigned to each vertex. I now want to visualize this data (so I can if these module reflect specific neuroanatomical structures), but I'm not sure about how to do this. Does anyone know how to do this? I tried to make a new color table, with my different module colors as the structures. I don't know how to then incorporate this information so that I can view it. I've read the tutorials on the label and annotation files, but I have only become more confused. If anyone can help me with this problem, I'd be very greatful! Thank you, Maria -- Maria Jalbrzikowski, Ph.D. Department of Psychiatry & Biobehavioral Sciences University of California, Los Angeles

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Re: [Freesurfer] kvlQuantify naming problem [possible fix]
by C.P. Frost 21 May '14

21 May '14

Follow-up: I then run into indexing problems when calling freeview with subfield volumes (similar to http://bit.ly/1pdEWRZ) which leads me to believe kvlQuantify is the only script that relies on the old convention. Changing the names back to CA2_3.mgz, etc., fixes THAT problem. Rather than changing the filenames to the old convention, it's probably better to fix the script and leave the filenames alone. On Wed, May 21, 2014 at 1:06 PM, C.P. Frost <carfro(a)gmail.com> wrote: > Hello all, > > My site has recently upgraded to the newest version of Freesurfer, and > I've run a set of subjects on recon-all using the hippocampal subfield > segmentation flag. Everything went well. Then in running > kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages > indicating that certain expected files didn't exist. > > In particular, among output files labeled with the scheme > $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and > ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz > -- in other words, the script expected a hyphen but instead the filenames > contained an underscroe. > > After renaming the files appropriately, kvlQuantify... successfully > generated the nonPartialVolumeStats files and everything worked fine. > > I didn't see any threads with this solution, and only one or two that > mentioned the problem (http://bit.ly/1vHbV5K) so I thought I'd offer it > up in case it could be addressed in a future release. > > Cheers, > C.P. Frost >

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Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
by Chung, Yoonho 21 May '14

21 May '14

Hi Anastasia, I have a large set of freesurfer recons (T1) already processed through FS version 5.2 longitudinal stream while ago. However, I see now that there is an advantage of using Tracula 5.3 longitudinal stream for DTI longitudinal analysis. Do you know if I run the DWI data using 5.3 TRACULA longitudinal stream - if it will work with recons that are processed with 5.2? Thanks! Y

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