Freesurfer

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30088 discussions

Monte Carlo Simulation algoritm for multiple comparisons correction
by Alexander Ivanov 03 Nov '11

03 Nov '11

*Dear Freesurfer Users and Developers, * Could you please help me to clarify the key steps implemented into the Monte Carlo approach for multiple comparisons correction? As far as I understood, it consists of running many permutations for fitting the measurements of different ROI sizes, which are being selected randomly according to predefined p-value. The process stops when optimal cluster is found and as a result we have the clusters of difference with clusterwise p-value and 90% C.I.... Am I wrong? Thank you very much beforehand... Regards, Alexander Ivanov

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right orbitofrontal cortex uncorrect segmentation
by _andreia_＠sapo.pt 03 Nov '11

03 Nov '11

Hi all, I'm getting this problem is many subjects (see attached files). As you can see the wm is not being properly classified. Adding control points or editing the wm file usually works, however I would like to know if this is usual and if there is a way to avoid the need for always manually correct this defect. Andreia

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Tracula Question, step 2
by Shannon Buckley 02 Nov '11

02 Nov '11

Hi Anastasia, I am trying to run Tracula for the first time in our lab and I'm getting errors during step 2 that seem to involve how the program wants to be launched via grid. I've attached the configuration file I'm using and the error message is below... _____ $trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh Using Freesurfer version 5.1. Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/ Sessions Directory is /home/vhasfcbuckls/sessions INFO: SUBJECTS_DIR is /cind/07/PPMI/Freesurfer/subjects INFO: Diffusion root is /cind/00/PPMI/Freesurfer/Tracula Actual FREESURFER_HOME /cind/01/apps/freesurfer/64bit/freesurfer5.1 ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dlabel/diff/anat_brain_m ask.bbr.nii.gz /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.ni i.gz ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/dwi.nii.gz /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri subjectdir is /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue "short.q". Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue "long.q". Exiting. Queuing post processing stage Unable to run job: denied: "60" is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue "long.q". Exiting. _____ Although we DO have a grid, I am trying to test the program for feasibility purposes, just on my own system's terminal, since we aren't sure how results will look with our specific data set (3.0 Tesla Siemens, 64 directional DWI @ b=1000, with 1 b0 image). We are very interested in performing tractography in T1-space. I am open to running this over the grid, if that's really the best way to do it, but the problem is that I don't see anywhere to specify the name of the queue that should be used for launching the program. Can you please tell me how to launch this without using the so-called long.q and short.q? We typically launch jobs to our grid using our "bash.linux.q", but I haven't been able to locate a place in the configuration file, or any switches to use in the cmd line, to specify that this queue should be used. I tried specifically launching Tracula's step 2 onto our bash.linux.q via the cmd line using "qsub", but received the same old error I had been getting. I checked the data independently using "bedpostx_preproc.sh", and it appears that all the required data are set up properly. As far as I can tell, the only issue we have is this inability to use the long.q and short.q. What do you think? I've cc'd our IT specialist, Henry Mensch, who oversees our grid system in case you need someone to chime-in with any specific information about how our Linux systems are set-up. Thanks very much for your time, Shannon T. Buckley SRA III - Supervisor CIND, UCSF 4150 Clement St. (114M) San Francisco, CA 94121 Phone: (415) 221-4810 x4251 Fax: (415) 386-3954

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concerns about symbolic links during processing
by Vy Dinh 02 Nov '11

02 Nov '11

Dear experts, We have recently encountered processing errors (during recon-all and -autorecon2&3) due to the creation of symbolic links within our SUBJECTS_DIR. Since our data were located on a data mount, the system somehow could not source the linked file. We have addressed this issue by directly copying fsaverage and th *EC_average files directly to our current SUBJECTS_DIR so that the symbolic links did not need to be created. However, this brings to light some another concern. The subjects for our study were processed on a local computer and then copied to the server so that they could be processed on multiple computers. Since we wanted to keep a copy of the "raw" reconned data, we copied these subjects to another directory and proceeded to do manual edits. Are there other symbolic links created within the subjects directories or SUBJECTS_DIR that would become defunct with these copies? I read a post in the Freesurfer forum that the link to fsaverage (and other folders) were only created during recon-all for display purposes. However, when running group analyses, these folders/files will need to be accessed, so does that mean that we would have to change the path info in these links? Would you caution against moving the subject directories after recon-all has been run? Rather than all the steps in run recon-all again, are there specific functions that will recreate these links? Thanks, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh(a)rush.edu<mailto:Vy_dinh@rush.edu>

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Multiple sclerosis lesions
by Carolina Valencia 02 Nov '11

02 Nov '11

Dear FS users, I would like to use FS to calculate WM hypointensitis (so-called black holes) for patients with multiple sclerosis, but 1. I don't know which stat file I should use to report the volumes, such as total WM, WM hypointensities, etc 2. which editing tool I must use when the lesion is not classified as WM hypointensities by FS? I know that the control points are not used or recommended for WM lesions 3. Can I use other sequences for detecting other classes of lesions present in this disease, such as hyperintense T2 lesions (T2WI) or enhacing lesions on contrast enhaced MR, in order to calculate the volumes of those, or just the T1 (MPRAGE) 4. which literature do you suggest for the post processing of these lesions using FS or perhaps another tool? thanks a lot, Carolina

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propagating labels to gray matter
by David Grayson 02 Nov '11

02 Nov '11

Hi freesurfer experts, I currently have a set of cortical labels that are the result of a high-resolution parcellation of the standard aparc.annot labels (via the ‘connectomemapper’ software). I would like to extract the gray matter ROIs that correspond to these labels, and I understand that this requires a method to ‘propagate’ these labels through the gray matter. I have so far been unsuccessful – ‘mri_label2vol’ seems to only give me that pial or white surfaces, as opposed to the gray matter bodies. Does anyone know how to accomplish this? Thank you very much, David Grayson

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Re: [Freesurfer] propagating labels to gray matter
by Douglas N Greve 02 Nov '11

02 Nov '11

Hi David, an easy way is to load the segmentation as both a segmentation and as the auxiliary volume (not aux segmentation). When you click on a point, you'll see the number of the segmentation in the aux field of the control window. doug David Grayson wrote: > Hi Doug, > > I made good progress based on your suggestion of using mri_aparc2aseg. The last piece is that I need to understand what the index values of my output volume file correspond to. Here's the command I used: > > mri_aparc2aseg --s subID --annot myaparc --o TEST.nii.gz > > Although I did notice that the index values in TEST.nii.gz for the cortical ROIs in the RH are just above 2000, and just above 1000 for the LH, the values don't seem to match the labels in FreeSurferColorLUT.txt. Then again, that makes sense, because this is a custom label set, so they don't really exist in FreeSurferColorLUT.txt. > > How can I learn more about how the index values are being assigned? > > Thanks very much for your help, > > David > > P.S. I don't know if it will work, but I attached the aparc and volume files if it's necessary for you to look that those > > -----Original Message----- > From: Douglas Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Monday, October 31, 2011 7:40 PM > To: David Grayson > Cc: 'freesurfer(a)nmr.mgh.harvard.edu' > Subject: Re: [Freesurfer] propagating labels to gray matter > > Hi David, you can use mri_label2vol with the --proj option. This works > ok, but it is often not great. Another way (the way that aparc+aseg) is > created is to convert your label into an annotation, then use > mri_aparc2aseg. > > doug > > On 10/31/11 7:22 PM, David Grayson wrote: > >> Hi Doug, >> >> Although in principle, yes this is the idea, we have a set of labels that aren't actually in the aparc+aseg file (basically a set of high-density subdivisions of those regions). The only problem is that the labels I have are just in "surface-land." I am wondering, once I have the surface labels, is there a way to re-propagate them back into the gray matter? >> >> Thanks again, >> >> David >> >> -----Original Message----- >> From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >> Sent: Monday, October 31, 2011 2:38 PM >> To: David Grayson >> Cc: 'freesurfer(a)nmr.mgh.harvard.edu' >> Subject: Re: [Freesurfer] propagating labels to gray matter >> >> Do you just want the label in the orig volume space? If so, just use the >> labels in aparc+aseg.mgz >> doug >> >> David Grayson wrote: >> >>> Hi Doug, >>> >>> /path/to/FREESURFER/label/regenerated_lh_36$ mri_label2vol --label lh.bankssts.label --temp ../../mri/orig.mgz --identity --o TEST.nii.gz >>> >>> Thanks, >>> >>> David >>> >>> -----Original Message----- >>> From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >>> Sent: Monday, October 31, 2011 2:04 PM >>> To: David Grayson >>> Cc: 'freesurfer(a)nmr.mgh.harvard.edu' >>> Subject: Re: [Freesurfer] propagating labels to gray matter >>> >>> what was your label2vol command line? >>> doug >>> >>> David Grayson wrote: >>> >>> >>>> Hi freesurfer experts, >>>> >>>> >>>> >>>> I currently have a set of cortical labels that are the result of a >>>> high-resolution parcellation of the standard aparc.annot labels (via >>>> the ‘connectomemapper’ software). I would like to extract the gray >>>> matter ROIs that correspond to these labels, and I understand that >>>> this requires a method to ‘propagate’ these labels through the gray >>>> matter. I have so far been unsuccessful – ‘mri_label2vol’ seems to >>>> only give me that pial or white surfaces, as opposed to the gray >>>> matter bodies. Does anyone know how to accomplish this? >>>> >>>> >>>> >>>> Thank you very much, >>>> >>>> >>>> >>>> David Grayson >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> 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. > -- 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

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pial area surface - correcting for size of brain
by Tetiana Dadakova 02 Nov '11

02 Nov '11

Dear FreeSurfer experts, I have a question regarding pial area analysis. What is commonly used as a nuisance variable to correct for brain size difference between groups (e.g men vs women)? Can you suggest any article where this is discussed or has been done? Thank you, Tanja.

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surface normals
by Oya, Hiroyuki (UI Health Care) 01 Nov '11

01 Nov '11

Dear Sir, Can the surface normals be loaded in matlab? Is there a code for that and what variable should I look at in surf dir? Thank you. HIroyuki ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

2 1

VGL error
by Jason Tourville 01 Nov '11

01 Nov '11

Hello FreeSurferers, I run tksurfer remotely from a linux machine running CentOS (Boston University) using Virtual GL/TurboVNC. I have been able to do this successfully for years but have recently encountered the following error when calling tksurfer: surfer: tkoInitWindow(RMAUT015) [VGL] ERROR: OpenGL error 0x0502 [VGL} ERROR: in readpixels - - [VGL] 624: Could not Read Pixels The error occurs after the tksurfer image window is started but before a brain surface is displayed. I have confirmed that the error does not depend upon what ssh tunneling tool I am using nor on what time of machine I am using locally. Does anyone have experience with this problem? Suggested solutions? Cheers, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-6181 Fax: (617)353-7755

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