Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all
Hi Stefano - You need to download the file dmri_5.1_snow_leopard.tar.gz from the wiki page, unzip it, and copy ALL the files that come out into the same directory where you copied the trac-all update. The trac-all update doesn't solve the memory issue, for that you need the executables in dmri_5.1_snow_leopard.tar.gz. I will be going on a short vacation for the rest of the week and will not be able to answer questions during this time unfortunately. If you don't manage to get through the tutorial independently by Monday, please send in your questions then. Best of luck, a.y On Wed, 6 Feb 2013, std...@virgilio.it wrote: Hi Anastasia, which is the forder where I should put leopard uploade? I try to put it in folder where trac-all lives, but when I re-run trac-all I obtain the same error: dmri_train(11214) malloc: *** mmap(size=159744) failed (error code=12)*** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 15th slice Cannot allocate memory Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 6-feb-2013 0.11 A: std...@virgilio.it Ogg: Re: R: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all Type which trac-all to find out where trac-all lives on your computer, then copy the update files there. On Wed, 6 Feb 2013, std...@virgilio.it wrote: Anastasia, thank you for your patience and kindness. I apologie but how can I use them, particularly trac-all updates. Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-feb-2013 23.58 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all See updates: http://www.freesurfer.net/fswiki/Tracula On Tue, 5 Feb 2013, std...@virgilio.it wrote: I delete it and I attached my last configuration file. This is the error after rerunning: dmri_train(11214) malloc: *** mmap(size=159744) failed (error code=12)*** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 15th slice Cannot allocate memory Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Feb 5 23:46:51 CET 2013 Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-feb-2013 22.53 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all Is there a line that says set trainfile = ... in your configuration file? If so please delete it. On Tue, 5 Feb 2013, std...@virgilio.it wrote: I set $TUTORIAL_DATA as setenv TUTORIAL_DATA /Applications/freesurfer/subjects/TUTORIAL_DATA In $TUTORIAL_DATA/diffusion_tutorial I do not found subj,train,difftutorial23.txtsubjI find subj,train,difftutorial32.txtsubj in $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-feb-2013 22.33 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: tracula and recon-all I'm guessing that there's some confusion about the instructions in the tracula tutorial and that you are settin the trainfile variable in your configuration file to look for a file in that directory. If so, just delete that line from your configuration file. On Tue, 5 Feb 2013, std...@virgilio.it wrote: Yes directory existbutnothereis lh.cst_AS.flt.trkin /Applications/freesurfer/subjects/TUTORIAL _DA TA /diff usion_tutorial/Diff0 01/ dlabel/mni/ Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 5-feb-2013 22.23 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] R: Re: R: Re: tracula and recon-all It's looking for files in /Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion Does this directory actually exist? On Tue, 5 Feb 2013, std...@virgilio.it wrote: Thank you very much Shantanu and Anastasia.Now I'm running trac-all but I have an error: niiRead():erroropeningfile/Applications/freesurfer/subjects/TUTORIAL_DATA/ d iffusion_t utori al/Diff 001/ dlabel/mni/lh.cst_AS_roi2.flt.nii.gz WARN:Couldnotopen/Applications/freesurfer/subjects/TUTORIAL_DATA/diffusion _ tutor ial/D iff 001/ dlabel/mni/lh.cst_AS.flt.trk for reading WARN: Error was: Can not open file WARN: Skipping to next subject dmri_train(5801) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region
Re: [Freesurfer] Difficult results from our PD data
Hi Bruce, I checked the surface of every subject with tksurfer, inaccuracy's were founded in 13 of 140 subjects. These subjects were manually edited with control points and pial edits. Then i start recon-all on the subjects with edits again. After these procedure tksurfer showed a correct segmentation. Is that the correct procedure for checking inaccuracy's? Or do i need to check more? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Many thanks, Stan From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 05 February 2013 15:54 To: Berg, S.F. van den Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Difficult results from our PD data Hi Stan we have found positive correlations between performance (in this case CVLT) and thickness, so it is certainly possible. And negative correlations aren't necssarily false - you could certainly imagine that successful pruning for example could help performance. Have you visually inspected the surfaces for accuracy? cheers Bruce On Tue, 5 Feb 2013, Berg, S.F. van den wrote: Dear Freesurfer experts, We investigated the relation between cortical thickness and performance on several cognitive tasks within a large group of Parkinson?s disease patients, but are slightly puzzled by the results. We obtained several, both in the vertex-wise analysis in qdec and in the SPSS analysis in the a-priori parcelated areas, negative correlations (i.e. better performance relates to a thinner cortical area) for all our neuropsychological tasks. These negative correlations were unexpected and we are having a hard time interpreting them. After correcting for multiple comparisons, all effects failed to reach the statistical threshold, rendering no results at all. When we compared our patient group on a structural level with healthy controls, we did find expected results that made sense. We also ran the exact same analyses (same group, same data) in VBM and there found several positive task-related correlations in expected areas. We noticed that in previous literature almost no studies investigated the relation between cortical thickness and cognitive task-performance. This made us wonder whether Freesurfer is suited for these correlation-based analyses, or is it better to be used in between group analyses? And do you have any idea on how to explain our negative correlations? Is it possible we might have done something wrong? Many thanks, Stan 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Qdec
I never received a reply, so I am reposting my message below. Any help would be greatly appreciated. Thanks in advance, Crystal On 2/4/13 10:35 AM, Franklin, Crystal G frankl...@uthscsa.edu wrote: So I ran mri_surf2vol --help and I am still a little confused on what to run. Where do I actually give the sig.mgh file? All the options seem to ask for an individual subjects file. Thanks, Crystal On 2/1/13 5:57 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You can run it with --help to get more info, let me know if you have questions after that On 02/01/2013 05:08 PM, Franklin, Crystal G wrote: Which options should I use when running mri_surf2vol? Crystal On 2/1/13 1:08 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: QDEC will create an output folder. In that folder, there will be a folder for each contrast. In the contrast folder, there will be a sig.mgh file. this has the -log10(p) significance values. You can convert this to nifti with mri_convert, but it will still be on the surface. If you need it in a volume, you can use mri_surf2vol doug On 02/01/2013 09:34 AM, Franklin, Crystal G wrote: Freesurfer, I ran a group comparison using qdec and got my results showing the differences in the thickness between the groups. I want to take these results I see in the viewer and convert them to nifti format so I can use them in another software called MANGO. Which files do I need to convert that shows the contrast differences? Thank you, Crystal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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 gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] nu_estimate_np_and_em error during recon-all
Tudor, Sorry to hear its not working. There is a plan B: scrap our VirtualBox instance entirely and instead install FSL's VMWare (from their website). This has a 64b Centos, so upon successful installation of it, you would download our 64b centos freesurfer distribution. Nick On Wed, 2013-02-06 at 12:59 +, Tudor Popescu wrote: ..I also did the following in the meantime, to make sure that the problem isn't due to a path error: - ran nu_estimate_np_and_em and nu_correct: both seem to respond fine, and they return their version number - checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point into $FREESURFER_HOME/mni , as they should Still cannot get recon-all to run because of the error mentioned previously currently at my wit's end! :( On 4 February 2013 10:29, Tudor Popescu tud...@gmail.com wrote: Hi NIck, I too thought disk space might be an issue, however I''ve been running the recon-all from a mounted partition (shared folder in Virtualbox) that has plenty of space: FreeSurfer:~ df -h FilesystemSize Used Avail Use% Mounted on /dev/sda1 11G 9.8G 0 100% / tmpfs 755M 0 755M 0% /lib/init/rw varrun755M 104K 754M 1% /var/run varlock 755M 0 755M 0% /var/lock udev 755M 152K 754M 1% /dev tmpfs 755M 0 755M 0% /dev/shm lrm 755M 2.4M 752M 1% /lib/modules/2.6.28-11-generic/volatile overflow 1.0M 12K 1012K 2% /tmp Dell 173G 106G 68G 62% /media/Dell The list of commands I ran were: sudo mount -t vboxsf Dell /media/Dell setenv SUBJECTS_DIR /media/Dell/_FS/buckner_data/tutorial_subjs recon-all -s bert -all THis is because running it from the home (default) partition was not possible, as it has 0 KB free space, and the discussion with Virtualbox support, where I asked how to increase it, has not been very helpful. Tudor On 31 January 2013 18:42, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Tudor, I'm a bit at a loss as to why it wont work. It appears you have plenty of available memory. Also, another person on the list confirmed that bert will run to completion in the fsv5.1 WindowsVM. I noticed though that it appears you have the buckner tutorial data. I dont have my virtual machine on hand to check the available disk space reserved for it, but check that you have enough disk space. run 'df -h'. or just delete some of the tutorial subjects and try again. This might be the problem since you mentioned you were having problems with recon-all.log file creation. Nick Thanks Nick, I ran the rm command and then re-ran recon-all. Got the same error, but at least now recon-all.log was created, see attached. Tudor On 31 January 2013 17:16, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Tudor, the log indicates that you need to run this: rm /media/Dell/_FS/buckner_data/tutorial_subjs/bert/scripts/IsRunning.lh+rh to get recon-all to run again. Nick Hi Nick, Thanks for your reply! I increased the memory available to FS in the virtualbox to the maximum allowed value (80% of my machine's total RAM), such that the free command returns: total used free sharedbuffers cached Mem: 2838372 5223042316068 0 11176 37663 Virtualbox support advised me to not increase this memory to more than 1GB (of my total 4GB), as this would lead to system
Re: [Freesurfer] Memory Consumption of GPU-assisted Freesurfer?
The environment variable 'FREESURFER_CUDA_DEVICE' defines the device number of the GPU device. Although I dont think you will see much benefit in splitting the surface processing across two gpus, as the CUDA surface code is not as optimal as the volume-based mri_ca_register code for parallel processing. Nick On Mon, 2013-02-04 at 19:31 -0500, R Edgar wrote: On Mon, Feb 4, 2013 at 6:54 PM, Zhongtian Dai d...@uchicago.edu wrote: Thanks for the speedy response. I think we will go with GTX 660 Ti with 2GB GPU RAM. We don't have a lot of subjects (as we hope to have) to analyze, so maybe we will try splitting left and right hemispheres to two graphic cards if our CPU RAM doesn't deplete. How do you designate the cuda commands to a certain GPU? You'll have to ask Nick that - I don't remember, I'm afraid. Richard ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] invalid=766 recon-all
None of the text in bold is of concern. It appears that mri_ca_register was running, which can take many hours to complete. Nick On Mon, 2013-02-04 at 22:55 +0100, std...@virgilio.it wrote: Hi list, I'm running : recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_sub001 In bold the error that I'm visualizing: Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff01 Actual FREESURFER_HOME /Applications/freesurfer Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001 \n mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998454, 0.00426797, -0.0554224) j_ras = (0.0151969, 0.980022, -0.198308) k_ras = (-0.0534688, 0.198844, 0.978572) writing to /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz... # #@# MotionCor Mon Feb 4 20:34:08 CET 2013 Found 1 runs /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. \n cp /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz \n /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001 \n mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz --conform \n mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998454, 0.00426797, -0.0554224) j_ras = (0.0151969, 0.980022, -0.198308) k_ras = (-0.0534688, 0.198844, 0.978572) Original Data has (0.8, 2, 0.8) mm size and (320, 85, 320) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz \n INFO: extension is mgz # #@# Talairach Mon Feb 4 20:34:17 CET 2013 /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri \n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n # #@# Talairach Failure Detection Mon Feb 4 20:34:49 CET 2013 /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4903, pval=0.1531 = threshold=0.0050) \n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/transforms/talairach_avi.log \n TalAviQA: 0.96699 z-score: -2 # #@# Nu Intensity Correction Mon Feb 4 20:34:50 CET 2013 \n mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 \n /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri /Applications/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Darwin
Re: [Freesurfer] Qdec
something like mri_surf2vol --surfval sig.mgh --hemi lh --identity fsaverage --o sig.lh.vol.nii.gz doug On 02/06/2013 09:50 AM, Franklin, Crystal G wrote: I never received a reply, so I am reposting my message below. Any help would be greatly appreciated. Thanks in advance, Crystal On 2/4/13 10:35 AM, Franklin, Crystal G frankl...@uthscsa.edu wrote: So I ran mri_surf2vol --help and I am still a little confused on what to run. Where do I actually give the sig.mgh file? All the options seem to ask for an individual subjects file. Thanks, Crystal On 2/1/13 5:57 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You can run it with --help to get more info, let me know if you have questions after that On 02/01/2013 05:08 PM, Franklin, Crystal G wrote: Which options should I use when running mri_surf2vol? Crystal On 2/1/13 1:08 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: QDEC will create an output folder. In that folder, there will be a folder for each contrast. In the contrast folder, there will be a sig.mgh file. this has the -log10(p) significance values. You can convert this to nifti with mri_convert, but it will still be on the surface. If you need it in a volume, you can use mri_surf2vol doug On 02/01/2013 09:34 AM, Franklin, Crystal G wrote: Freesurfer, I ran a group comparison using qdec and got my results showing the differences in the thickness between the groups. I want to take these results I see in the viewer and convert them to nifti format so I can use them in another software called MANGO. Which files do I need to convert that shows the contrast differences? Thank you, Crystal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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 gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Xhemi questions
Dear Doug and FreeSurfer experts,Thnak you so much for all your lasts responses!.I did ran succesfully all the pre-processing for the interhemispheric comparisons on FS. Now I have a couple questions:given the command for interhemispheric comparisons:mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir glm.lh.lh-rh.thickness.sm05 --osgm --surf fsaverage_sym lh;A) This read all subjects to construct X and C as one-sample group mean, this means that as result I get the difference across hemispheres and across my subjects in a population, right? B) But, what if I have two groups? controls and patients, I'm wondering if is it possible to examine regional differences of thickness asymmetries between those two groups? or more?C) If I want to examine effects of group or sex, while controlling for age and other factors how do I introduce them into the glm model? If so, do I set the contrasts as normally for mri_glmfit? I mean as any other thickness study? or there is any other thing that I should do?The command for multiple comparisons correction is:mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 --cwpvalthresh .5 --cache 2 absWhich performs only cluster-wise corrections, D) is there any other way to correct for multiple comparisons, something like permutation tests or anything else?Many thanks in advanced,Gabriel ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Problem with flip4fsl
Hi FreeSurfer community, I am trying to run 'trac-all -corr -c config file' on the tutorial data, specifically for the single subject: Diff001. To start from 'scratch', I've deleted all but the './scripts' and the './orig' directories in the Diff001 parent folder. When I run the following command: trac-all -corr -c config file I receive the following error: ERROR BEGINS flip4fsl /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig.nii.gz /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 fslswapdim /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig.nii.gz x -y z /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz Cannot open volume /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi_orig_flip for reading! ERROR ENDS Looking in my 'Diff001/dmri' directory, I cannot locate a 'dwi_orig_flip.nii.gz' file. I assume this is where the script breaks. I tried to run the 'flip4fsl' command singly, but received the same error. I'm working on a: 3.2.0-35-generic #55-Ubuntu SMP Wed Dec 5 17:42:16 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux I've unsuccessfully searched through the mailing list archive to find if others had encountered the same issue previously. Does anybody have any suggestions? Thanks! Susie ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Troubleshooting the preproc
Hi FreeSurfer community, I am currently trying to troubleshoot my preprocessing part of TRACULA with the tutorial dataset (for *Diff001* as the subject, specifically), running *trac-all -corr -c config dmrirc*. I am running the commands in * subjectID/scripts/trac-all.cmd* one by one because I've had problems with some of the steps. Specifically, *flip4fsl* didn't work. I instead used *fslswapdim -x -y z* (*flip4fsl* uses *fslswapdim x -y z*, which doesn't generate the correct orientation for FSL in fact), followed by *fslorient -forceradiological*. I successfully ran *eddy_current *thereafter. Now I am stuck again, at FreeSurfer's *xfmrot, *which should look like: * * *xfmrot transform file input vector file [output vector file]* I specifically typed in: *xfmrot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi.ecclog /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs.norot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs* and received the following iterative errors: * avscale: Command not found. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. * Can any of you help me? Thank you, Susie K ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Difficult results from our PD data
Hi Stan, the VBM results may be picking up changes in GM volume. These volume changes may be driven by differences in surface area and would not necessarily show up in a thickness analysis. Maybe the surface area is increasing with performance but the thickness is decreasing. You can do a surface-based analysis of surface area and/or volume (this is similar to a VBM analysis but on the surface). You can do this by specifying --meas area or --meas volume to mris_preproc. Make sure you have the mris_preproc patch (or are using 5.2). doug On 02/05/2013 09:54 AM, Bruce Fischl wrote: Hi Stan we have found positive correlations between performance (in this case CVLT) and thickness, so it is certainly possible. And negative correlations aren't necssarily false - you could certainly imagine that successful pruning for example could help performance. Have you visually inspected the surfaces for accuracy? cheers Bruce On Tue, 5 Feb 2013, Berg, S.F. van den wrote: Dear Freesurfer experts, We investigated the relation between cortical thickness and performance on several cognitive tasks within a large group of Parkinson?s disease patients, but are slightly puzzled by the results. We obtained several, both in the vertex-wise analysis in qdec and in the SPSS analysis in the a-priori parcelated areas, negative correlations (i.e. better performance relates to a thinner cortical area) for all our neuropsychological tasks. These negative correlations were unexpected and we are having a hard time interpreting them. After correcting for multiple comparisons, all effects failed to reach the statistical threshold, rendering no results at all. When we compared our patient group on a structural level with healthy controls, we did find expected results that made sense. We also ran the exact same analyses (same group, same data) in VBM and there found several positive task-related correlations in expected areas. We noticed that in previous literature almost no studies investigated the relation between cortical thickness and cognitive task-performance. This made us wonder whether Freesurfer is suited for these correlation-based analyses, or is it better to be used in between group analyses? And do you have any idea on how to explain our negative correlations? Is it possible we might have done something wrong? Many thanks, Stan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] aparc2aseg for an averaged subject
Hi Paul, try this cd $SUBJECTS_DIR/youraveragesubjectname mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon youraveragesubjectname doug On 02/04/2013 02:40 PM, Paul Beach wrote: Hi Doug, Your suggestion to remove the 'unknown' label when using the mris_label2annot command worked like a charm. Thanks! However, now I'm trying, as per your original advice, to re-run mri_aparc2aseg in order to get my labels to fill out the entire cortical ribbon (with the end goal of exporting these labels/ROIs to AFNI). I tried this on my averaged subject (created with 'make_average_subject') and it gave me the error that there is no ribbon.mgz file in the mri folder. Upon checking the mri folder, there is indeed no 'ribbon.mgz' file. Looking at the options for 'mri_aparc2aseg' on the wiki it doesn't look like there's any way around this problem from that angle - at least from the perspective of using my averaged subject. In the averaged subject's mri folder there are only the following files: aseg.mgz brain.mgz orig.mgz T1.mgz brainmask.mgz mni305.cor.mgz p.aseg.mgz Interestingly, in the fsaverage subject there are ribbon.mgz files. Is there a way to make a ribbon.mgz file for averaged subjects?? Thanks, Paul On Thu, Jan 31, 2013 at 2:12 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Paul, this mostly looks right. I think the problem may be that you are including the unknown label on the command line. I think that mris_label2annot will ignore the 0 inthe ctab file, which means that it assign the first label passed (lh.unknown.label) to the the first non-zero ROI in the ctab file (banksts). Try that and see if it works. doug On 01/30/2013 03:03 PM, Paul Beach wrote: Hi Doug, I've been attempting to utilize the programs suggested by you to create manual labels (ROIs) on the cortical surface of tksurfer to be able to export certain ones to AFNI. The problem I was having originally was that the cortical ribbon was not fully covered by surface drawn labels that were changed to volumes by MRI_label2vol. You suggested first using mri_annotation2label to extract the labels within the aparc.annot files (left and right hemispheres), putting my created labels into the same folder (replacing, for example, the insula label with anterior, middle, and posterior insula labels) and then using mris_label2annotation to make a new annotated file to be sent into a re-ran mri_aparc2aseg. The problem I'm running into now, after extracting all the labels, putting in my own, and running mris_label2annotis that the resultant annotation's labels are highly out of place and disorganized. For example, the label for the cuneus is where the corpus callosum is. I'm wondering if this has something to do with the order of labels in the mris_label2annot script of possibly with my .ctab file. The latter was created based on what I found here https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit on the Freesurfer wiki. I simply added my six manual labels/ROIs at the end. I tried to use their GWFSAnnotToLUT https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit?action=AttachFiledo=viewtarget=GWFSAnnotToLUT program, but could not get it to work, so I'm not sure if the .ctab file accurately represents tksurfer's Lookup Table. I'm also not sure if it has something to do with overlapping vertices of different labels. For example, will leaving the insula label in mess things up when I also try to include the anterior, middle, and posterior insula labels? If so, would simply removing labels that overlap, vertex-wise, help? I have attached the setup of the .ctab file as well as my mris_label2annot script. Thanks for your advice, Paul On Tue, Jan 22, 2013 at 2:52 PM, Paul Beach pabea...@gmail.com mailto:pabea...@gmail.com mailto:pabea...@gmail.com mailto:pabea...@gmail.com wrote: Thanks for your help! On Tue, Jan 22, 2013 at 11:12 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: mri_annotation2label breaks them appart mris_label2annot puts them back together again doug On 01/22/2013 11:09 AM, Paul Beach wrote: Hi Doug, Thank you for this. However, can you give me a hint as to
Re: [Freesurfer] FDR threshold on functional data
Hi Susan, try right clicking in the display window to remove the marks from the label. doug On 02/04/2013 03:08 PM, Susan Alice McLaughlin wrote: Hi, I am looking at functional group surface data analyzed with mri_glmfit in tksurfer (using Freesurfer 4.1). I would like to threshold using FDR - but only within a specified label - and then see the resulting functional data map. Once I have the functional dta loaded as an overlay, I have been loading my label and marking the selected label under the Tools menu. I then set the threshold using FDR only on marked data. So far, so good. However, once this is done, I have not been able to see the thresholded functional map in the label; I can only the whole area in white, marked. How do I see my functional data map? I apologize for this simplistic question; I have not been able to find a solution looking through the tksurfer guides online or the mail archives. Thanks, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Multi-voxel pattern analysis
Hi, I am very new to FreeSurfer, but would like to start using it for my research. In particular, I would like to know if I could do MVPA with FreeSurfer? Thanks. Luísa ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Multi-voxel pattern analysis
Hi Luisa yes, Mert Sabuncu and Koen Van Leemput have developed a MVPA algorithm called RvoxM that I believe is state-of-the-art in terms of classification accuracy. Perhaps they can point you in the right direction? cheers Bruce On Thu, 7 Feb 2013, Luísa Pinto wrote: Hi, I am very new to FreeSurfer, but would like to start using it for my research. In particular, I would like to know if I could do MVPA with FreeSurfer? Thanks. Luísa ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mrisReadTriangleFile failed
Just had a cluster of computers lock up, unfortunately resulting in several freesurfer jobs terminating prior to completion. It's possible I may have a ton of this same error come tomorrow. Two questions 1) is there a way to tell if a surface is out of date without starting up tkmedit? 2) last time I ran -make all, the command line disappeared until the job completed. This never happens when I run recon-all with autorecon23. Anyway to avoid this? jon On Feb 1, 2013, at 1:28 PM, Jonathan Holt wrote: OK, good deal! The first time I ran recon-all it exited with errors. That must be the issue. thanks, jon Hi Jon that means that one of the surfaces is out of date, usually because you edited and reran but not to completion. Try running recon-all -s subject -make all cheers Bruce p.s. ignore the can't find file thing. It really means it tried to read it, but found it wasn't the same topology as the other surface and that's what it is complaining about On Fri, 1 Feb 2013, Jonathan Holt wrote: Experts, Having an issue with this error. It's complaining about rh.pial not matching rh.white, indicates there's no such file or directory and that mrisReadTriangleFile failed, and then proceeds to load without rh.pial. I tried loading rh.pial manually, but upon loading it immediately removes every surface on the LH. Wasn't an issue before I ran recon-all. Worth noting this brain was generated from a particularly low contrast MRI scan, and freesurfer had trouble generating correct surfaces from the get go. Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
