Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

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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surface-based morphometry registration
by Tudor Popescu 21 May '14

21 May '14

Hi all, If I understand correctly, the surface-based morphometry (SBM) done by Freesurfer offers superior registration as compared to voxel-based methods such as VBM, in that: 1. "SBM smoothing respects anatomical boundaries better than the 3D VBM smoothing". 2. "SBM group analysis employs inter-subject alignment based on the patterns of sulci and gyri, as opposed to Talairach registration, which often ignores sulcal/gyral landmarks" I'm not sure I understand those reasons, however. For 1., why does the smoothing operation (basically, a multiplication) "care" about anatomy or registration at all, such that it can be said it is better done in SBM vs VBM? And for 2., doesn't the Talairach registration used in VBM simply imply a certain target template? Surely such a template is used in SBM registration as well, and if that is the case, then how are sulcal/gyral landmarks taken into account? Thanks for any help! Tudor

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mri_convert frame error in tracula
by Pedro Rosa 21 May '14

21 May '14

Dear All, As suggested, I am reposting a previous question. I am trying to run a single subject in TRACULA (trac-all -corr -c config), 148, for who there is a folder ‘1482’ with all DWI DICOMs and a folder ‘ESNA148’ with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is bval.bval and bvec.bvec. I attached the trac-all.log that comes with the following error: ERROR: fMRIframe: frame >= frames Can anyone help me? Thank you in advance! Regards, Pedro Rosa.

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recon-all mri_nu_correct error
by Durai Arasan 21 May '14

21 May '14

Hi Freesurfer experts, I was running recon-all on a cluster and encountered the following error: mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux compute-g20-12.deepthought.umd.edu 2.6.18-371.3.1.el5 #1 SMP Mon Nov 11 03:23:58 EST 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s hcp80100307 exited with ERRORS at Wed May 21 12:43:36 EDT 2014 Any idea whats the source of the error? Thanks! On Wed, May 21, 2014 at 2:20 PM, C.P. Frost <cpfrost(a)wisc.edu> 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

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