Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Minor issues with Freesurfer v4.0.4/rerunning on 4.2.0
by John Sheppard 26 Jan '09

26 Jan '09

Hey everyone, I have finished anatomical segmentations on a batch of brains, however this was done in Freesurfer 4.0.4 and I realized several of my subjects have issues previously described here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-August/008266.h…, with MRIScomputeWhiteVolume. I didn't get as massive error.log files but they were maybe up to 1mb in size. I understand should be corrected by re-running recon-all -segstats -wmparc for those using ?h.cerebral-white-matter in aseg.stats or wmparc.stats. In the latest release bugs were also fixed so that wmparc.stats and aseg.stats volumes should match up. Does this update only increase the volumes in wmparc.stats (we aren't using that data anyway, but we are using aseg.stats) but leave aseg.stats the same? There was also the potential for spikes to occur in pial surface near insula in 4.0.4, though I inspected the segmentations and did not notice this problem. Other than those things, is there any serious need to re-run autorecon2 or 3 after having processed them through 4.0.4 previously? Sorry if I missed anything previously discussed, I had a look at the update release notes and tried searching the mailing list archives. Thanks! John -- John Sheppard Undergraduate Student Department of Biomedical Engineering Northwestern University Phone: (630) 957-8321 E-mail: john-sheppard(a)northwestern.edu Address: 1927 Orrington Ave. Rm 8203 Evanston, IL 60201

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DODS/DOSS choice in patient/control study
by Burmicz, Ryzarda 26 Jan '09

26 Jan '09

Hello, We are looking at patients versus control group analysis. We have done a straight analysis and are now looking at covariates. DOSS produces similar results to a straight patient vs control analysis, in that some blobs are located in the same cortical regions. In the case of DODS, there is no similarity whatsoever to the straight analysis maps... which is why I am so stuck in deciding, because it really does impact on the results quite drastically. I understand the difference between DODS and DOSS - and I know the following question is not an easy one to answer, however we have sample sizes of 15 patient vs 15 control subjects and would like to know if that is great enough such that we are better off going for DODS. There is no reason to say that the patient cortical thickness - age relationship is any different in slope from that of normal ageing generally; however in certain cortical regions patients exhibit a thickening of the cortex, and thinning in other (albeit fewer) regions. Do you have any comments? I would have thought that our sample sizes are rather small, but would appreciate your input. I attach the comparison of patient vs control covaried for age under both DODS and DOSS to illustrate the differences. Thanks! Rysia Ryszarda Burmicz Research Assistant Centre for Neuroimaging Sciences PO89 Institute of Psychiatry

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Re: [Freesurfer] Freesurfer 4.0.5 Leopard
by Ming Hsu 26 Jan '09

26 Jan '09

Hi Nick, I was able to download 4.0.5, and everything runs fine on the desktop. However over ssh, qdec seems to crash the x server. The program would begin loading, and it appears for a second then the error: X connection to localhost:10.0 broken (explicit kill or server shutdown). After that I have to restart my laptop to run any X applications. BTW, the same thing seems to happen on 4.1. Thanks, Ming On Tue, 13 Jan 2009 07:34:49 -0800, Nick Schmansky wrote: > Ming, > You can get it here: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable > notice there is one for intel and one for powerpc. > Nick -- Ming Hsu Department of Economics, and Beckman Institute for Advanced Science & Technology University of Illinois at Urbana-Champaign Office: (217) 244-1122

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Calcarine fissure is divided into parts in the flat map
by Jürgen Hänggi 26 Jan '09

26 Jan '09

Dear FS experts The calcarine fissure (shown in cyan) is divided into several parts in the flat map. All other areas are still in one part in the flat map (see attachment). Is there anything wrong or is this the consequence of setting the relaxation cut in the calcarine fissure? Thanks in advance Regards Jürgen ---------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------

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how to export volumes of different regions after segmentation?
by Bai Xue 26 Jan '09

26 Jan '09

Hi, I have done recon-all. Is there a command or button that can export all different region volumes maybe to a txt file so that we can have a look and compare? Thanks. Bai Xue

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Warping label across mutliple brain surfaces
by Tony L 25 Jan '09

25 Jan '09

Hello, I have been unable to find a procedure/script to create a label based on talairach coordinates (or created on an averaged brain surface), and apply this label to different brain surfaces (e.g. warping the label to fit different brains). This is analogous to Freesurfer's built-in colored annotations depicting a surface's different brain cortices with labels. I need to do the exact same thing, but with a label that I define myself. Thank you very much! Best regards, Anthony _________________________________________________________________ Windows Live™ Hotmail®…more than just e-mail. http://windowslive.com/howitworks?ocid=TXT_TAGLM_WL_t2_hm_justgotbetter_how…

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Re: [Freesurfer] cropping of average T1
by Siddharth Srivastava 24 Jan '09

24 Jan '09

Hi Bruce, I just realised that the cropping at the posterior aspect is similar to the cropping usually done for the inferior aspect in a saggital view (to get rid of the neck etc..) . Could it be (remotely) possible that the cropping was done in a different orientation (nose pointing up in the sagittal view), and then oriented to the views that we see now? I have only used the basic commands "make_average_subject" with no special flags except --force sid. On Fri, Jan 23, 2009 at 10:33 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > I'm not really sure. Doug or Nick: any ideas? > > > On Fri, 23 Jan 2009, Siddharth Srivastava wrote: > > Hi Bruce, >> please find attached a tiff file generated by mri_concat >> --mean on the original mprages. >> Here i can see the full view, and i think no registration has been >> performed >> as yet on these >> images... Regarding exploring the dataset for 1 image, is it possible >> that >> just 1 rouge image >> can cause this problem? The clipping has a sharp border, almost as if the >> bounding box >> itself has been cropped at that level. the intensity in these posterior >> slices is zero. >> thanks, >> sid. >> >> On Fri, Jan 23, 2009 at 9:51 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> >wrote: >> >> if you can find a small set (1?) of subjects that generate the same >>> image, >>> then maybe you can just send us that subject and your commandline >>> >>> On Fri, 23 Jan 2009, Siddharth Srivastava wrote: >>> >>> ok.. i will try that and let you know... what other image/logs can i >>> >>>> provide >>>> for >>>> localizing the source of the error? >>>> sid. >>>> >>>> On Fri, Jan 23, 2009 at 9:04 AM, Bruce Fischl < >>>> fischl(a)nmr.mgh.harvard.edu >>>> >>>>> wrote: >>>>> >>>> >>>> not really, it seems like there is a bug. If you can localize it to >>>> just >>>> >>>>> one or a few subjects it would a lot easier to track down >>>>> >>>>> On Fri, 23 Jan 2009, Siddharth Srivastava wrote: >>>>> >>>>> Hi Bruce, >>>>> >>>>> These are about 28 images. I have not tried fewer...do you >>>>>> think there >>>>>> are some images with incorrect orientation in the cohort? That would >>>>>> show >>>>>> up >>>>>> in the other location in the average i think... >>>>>> sid. >>>>>> On Fri, Jan 23, 2009 at 8:46 AM, Bruce Fischl < >>>>>> fischl(a)nmr.mgh.harvard.edu >>>>>> >>>>>> wrote: >>>>>>> >>>>>>> >>>>>> I don't think so. How many subjects? Have you tried fewer? >>>>>> >>>>>> >>>>>>> On Fri, 23 Jan 2009, Siddharth Srivastava wrote: >>>>>>> >>>>>>> The surfaces look all right. It happens only to T1. It cant be a >>>>>>> display >>>>>>> >>>>>>> problem, can it?? >>>>>>> >>>>>>>> sid. >>>>>>>> >>>>>>>> On Fri, Jan 23, 2009 at 5:58 AM, Bruce Fischl < >>>>>>>> fischl(a)nmr.mgh.harvard.edu >>>>>>>> >>>>>>>> wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> that is strange. Do the surfaces look ok? How many subjects are >>>>>>>> you >>>>>>>> >>>>>>>> averaging? Does this happen if you only average one or a few? >>>>>>>> >>>>>>>>> >>>>>>>>> On Thu, 22 Jan 2009, Siddharth Srivastava wrote: >>>>>>>>> >>>>>>>>> Hi everyone, >>>>>>>>> >>>>>>>>> I am attaching a tiff file showing the tkmedit view >>>>>>>>> of >>>>>>>>> >>>>>>>>> the average >>>>>>>>>> T1 that freesurfer created during make_average_subject. I am a bit >>>>>>>>>> concerned >>>>>>>>>> >>>>>>>>>> about the cropping that is evident at the posterior aspect of the >>>>>>>>>> brain. >>>>>>>>>> The >>>>>>>>>> >>>>>>>>>> individual T1's are complete and ok, so i am guessing that >>>>>>>>>> something >>>>>>>>>> went >>>>>>>>>> wrong during the transform of the individual brain during the >>>>>>>>>> process. >>>>>>>>>> Can >>>>>>>>>> anyone help me find out the problem ? The average surfaces also >>>>>>>>>> look >>>>>>>>>> all >>>>>>>>>> right. >>>>>>>>>> thanks, >>>>>>>>>> sid. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>> >>>> >>

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Version 4.2.0 for Tiger on PowerPC Mac?
by Carl Anderson 23 Jan '09

23 Jan '09

Hi Would it be possible to somehow download V4.2.0 for Tiger running on a PowerPC Mac? Thanks ------------------------------------------------------- Carl M. Anderson, Ph.D. Assistant Professor of Psychiatry, Harvard Medical School & The Neural Imaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972 Fax: 617-855-2770 webpages: http://remfractal.mclean.org/main.html email: carl_anderson(a)hms.harvard.edu ------------------------------------------------------- Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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Cortical thickness conversion
by Yigal Agam 23 Jan '09

23 Jan '09

Hi, I'm trying to convert corical thickness maps into a common space and getting this error. Any ideas? mri_surf2surf --srcsubject mano002_new --trgsubject fsaverage --hemi lh --srcsurfval lh.thickness --trgsurfval /space/schnook/1/users/yigal/projects/dti/data/new_recons/mano002_new/surf/lh.thickness_fsaverage.nii --nsmooth-in 3 --nsmooth-out 3 srcsubject = mano002_new srcval = lh.thickness srctype = trgsubject = fsaverage trgval = /space/schnook/1/users/yigal/projects/dti/data/new_recons/mano002_new/surf/lh.thickness_fsaverage.nii trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /autofs/space/ventzl_001/users/SUBJECTS_DIR/mano002_new/surf/lh.sphere.reg Loading source data ERROR: dimesion inconsitency in source data Number of surface vertices = 115532 Number of value vertices = 118209 mri_surf2surf --srcsubject mano002_new --trgsubject fsaverage --hemi rh --srcsurfval rh.thickness --trgsurfval /space/schnook/1/users/yigal/projects/dti/data/new_recons/mano002_new/surf/rh.thickness_fsaverage.nii --nsmooth-in 3 --nsmooth-out 3 srcsubject = mano002_new srcval = rh.thickness srctype = trgsubject = fsaverage trgval = /space/schnook/1/users/yigal/projects/dti/data/new_recons/mano002_new/surf/rh.thickness_fsaverage.nii trgtype = surfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /autofs/space/ventzl_001/users/SUBJECTS_DIR/mano002_new/surf/rh.sphere.reg Loading source data ERROR: dimesion inconsitency in source data Number of surface vertices = 116029 Number of value vertices = 120919

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Fwd: [Freesurfer] cropping of average T1
by Siddharth Srivastava 23 Jan '09

23 Jan '09

---------- Forwarded message ---------- From: Siddharth Srivastava <siddys(a)gmail.com> Date: Fri, Jan 23, 2009 at 9:10 AM Subject: Re: [Freesurfer] cropping of average T1 To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> ok.. i will try that and let you know... what other image/logs can i provide for localizing the source of the error? sid. On Fri, Jan 23, 2009 at 9:04 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > not really, it seems like there is a bug. If you can localize it to just > one or a few subjects it would a lot easier to track down > > On Fri, 23 Jan 2009, Siddharth Srivastava wrote: > > Hi Bruce, >> These are about 28 images. I have not tried fewer...do you >> think there >> are some images with incorrect orientation in the cohort? That would show >> up >> in the other location in the average i think... >> sid. >> On Fri, Jan 23, 2009 at 8:46 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> >wrote: >> >> I don't think so. How many subjects? Have you tried fewer? >>> >>> On Fri, 23 Jan 2009, Siddharth Srivastava wrote: >>> >>> The surfaces look all right. It happens only to T1. It cant be a display >>> >>>> problem, can it?? >>>> sid. >>>> >>>> On Fri, Jan 23, 2009 at 5:58 AM, Bruce Fischl < >>>> fischl(a)nmr.mgh.harvard.edu >>>> >>>>> wrote: >>>>> >>>> >>>> that is strange. Do the surfaces look ok? How many subjects are you >>>> >>>>> averaging? Does this happen if you only average one or a few? >>>>> >>>>> On Thu, 22 Jan 2009, Siddharth Srivastava wrote: >>>>> >>>>> Hi everyone, >>>>> >>>>> I am attaching a tiff file showing the tkmedit view of >>>>>> the average >>>>>> T1 that freesurfer created during make_average_subject. I am a bit >>>>>> concerned >>>>>> >>>>>> about the cropping that is evident at the posterior aspect of the >>>>>> brain. >>>>>> The >>>>>> >>>>>> individual T1's are complete and ok, so i am guessing that something >>>>>> went >>>>>> wrong during the transform of the individual brain during the process. >>>>>> Can >>>>>> anyone help me find out the problem ? The average surfaces also look >>>>>> all >>>>>> right. >>>>>> thanks, >>>>>> sid. >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>

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Freesurfer