Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30083 discussions

cortical thickness maps
by Feng-Xian 28 Jan '09

28 Jan '09

Hi, Thank you for your help before. I finished the group analysis of cortical thickness with QDEC on FreeSurfer and I would like to get the cortical thickness maps with inflated surface on Windows XP. Would you teach me how can I change the cortical thickness maps from FreeSurfer to Windows XP? Thanks in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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Re: [Freesurfer] cropping of average T1
by Siddharth Srivastava 27 Jan '09

27 Jan '09

Hi bruce, This happens for every orig.mgz that passes through mri_convert at the start of make_average_volumes. The files are 9M each, is there a drop-area where i can upload them? I just made some checks: my orig/001.mgz files are LPS (primary->axial), while the converted files are LIA (coronal). Can this effect the result? In any case, if you send me the link to the drop area, i will put an example mgz. thanks, sid. On Sat, Jan 24, 2009 at 12:40 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Sid, > > can you send us the volume that has this happen? I think it's just a > display problem and won't affect anything else, but if you give us the > example we'll fix it. > > Bruce > > On Sat, 24 Jan 2009, Siddharth Srivastava wrote: > > Hi everyone, >> Has anyone faced this problem before? Is there an >> alternative >> to mri_convert than i can try to get the transformation, and then run the >> subsequent steps? Why are k_ras components approaching zero, and not >> exactly zero. make_average_surface works fine, no clipping, i have spent >> the >> >> last 20 or so odd hours checking each surf directory. This happens only >> for >> the >> structurals that pass through mri_convert. Tried changing the -oc >> values, there is a shift, as expected, but the clipping remains fixed at >> this level (hence more brain gets cropped if the -oc values shift the >> brain posteriorly. >> sid. >> >> >> >> On Fri, Jan 23, 2009 at 11:37 AM, Siddharth Srivastava <siddys(a)gmail.com >> >wrote: >> >> Hi bruce, >>> I think the offending command is >>> mri_convert /../../orig.mgz /../../orig-subject.mgh --apply_transform >>> /../../mri/transforms/talairach.xfm -oc 0 0 0 >>> I am attaching the pre- and post mri_convert as tiffs. I have also >>> attached >>> the pial_avg surface in the >>> posterior view, for you comments. >>> The folowing is the screen dump (patient name deleted): >>> >>> >>> ---------------------------------------------------------------------------------------------------- >>> $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ >>> reading from /../subject/mri/orig.mgz... >>> TR=1820.00, TE=2.93, TI=1100.00, flip angle=12.00 >>> i_ras = (-1, 0, 0) >>> j_ras = (0, 0, -1) >>> k_ras = (-9.31323e-10, 1, -1.49012e-08) >>> INFO: Applying transformation from file >>> /../subject/mri/transforms/talairach.xfm... >>> Reading transform with LTAreadEx() >>> --------------------------------- >>> INFO: Transform Matrix (linear_ras_to_ras) >>> 1.026 0.084 0.079 -9.471; >>> -0.105 1.048 0.228 -84.640; >>> -0.106 -0.174 1.165 -38.874; >>> 0.000 0.000 0.000 1.000; >>> --------------------------------- >>> Applying LTAtransformInterp (resample_type 1) >>> INFO: Transform dst volume info is not used (valid flag = 0). >>> applying the vox to vox linear transform >>> 1.026 0.079 -0.084 -1.205; >>> -0.106 1.165 0.174 9.576; >>> 0.105 -0.228 1.048 -61.401; >>> 0.000 0.000 0.000 1.000; >>> writing to /../../orig-subject.mgh... >>> ---------------------------------------------------------------------- >>> does this help in any way? >>> >>> thanks, >>> sid. >>> >>> >>> >>> On Fri, Jan 23, 2009 at 11:01 AM, Bruce Fischl < >>> fischl(a)nmr.mgh.harvard.edu >>> >>>> wrote: >>>> >>> >>> Hi Sid, >>>> >>>> have you looked through the individual datasets? That's where the >>>> cropping >>>> would be, which would have caused big errors in your surfaces. I assume >>>> that >>>> is not the case. >>>> Bruce >>>> >>>> >>>> On Fri, 23 Jan 2009, Siddharth Srivastava wrote: >>>> >>>> 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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Doubt about paradigm file and event related paradigm
by Francisco Robles 27 Jan '09

27 Jan '09

Hi, I'm Francisco Robles, from México city. I am using FS-Fast to analyze some event-related fMRI. My problem is jow to use the paradigm file because I need to exclude some images from my analysis. The situation is that I have a paradigm of 3.5 secs of stimulus and a variable quantity of Null/fixation. But from those 3.5 secs of stimulus, I only want to analyze the last 1.75 secs. The opseqt file I've got goes like this: 0.0000 2 3.500 1.0000 var1 3.5000 4 3.500 1.0000 var3 7.0000 4 3.500 1.0000 var3 10.5000 3 3.500 1.0000 var2 14.0000 0 1.750 1.0000 NULL And I edited it to look like this but I really don't know if it is the right way to do it: 1.75 2 1.75 1 "var1" 5.25 4 1.75 1 "var3" 8.75 4 1.75 1 "var3" 12.25 3 1.75 1 "var2" 14.00 0 1.75 1 "NULL" So I put in the column of stimulus onset, the time point I want to analyze and in the duration column, only the quantity of time I want to analyze. But I've seen in mkanalysis-sess.new on wiki, that there is a flag -tpef [filename] for the command selxavg3-sess that allows to exclude certain files according to a time-point, but I don't know how to do it, how is the arrange of taht file, how many columns, how do I say to it that I only want the last 1.75 secs and not the hole 3.5 secs. I am really lost, if anyone can help mw I will appreciate it a lot. Thank you all in advance. _________________________________________________________________ Comparte fotos, juega y charla en Messenger. http://download.live.com/messenger

1 1

Mean Curv
by Vina Goghari 27 Jan '09

27 Jan '09

Hello all, What is the mean curv in the stats files a measure of? Thanks kindly, Vina

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aseg.stats
by Kellen Mobilia 27 Jan '09

27 Jan '09

I would like to pose a brief question. Somehow in the process running brains through autorecon one of my subjects aseg.stats files became messed up and as far as I am able to tell everything else is intact. Is there a quick way to rebuild the data that is written to that file? Or do I have to re-run the autorecon sequence? Thanks Kellen

2 1

memory alloc problem in mri_fwhm
by Krishna Srihasam 27 Jan '09

27 Jan '09

Hi, I am analyzing my fMRI data and I got a memory alloc problem in "mri_fwhm" The exact message is : mri_fwhm --mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii --i /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/res/all.nii --sum /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.sum --dat /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.dat MRIalloc(96, 84, 33): could not allocate 32256 bytes for 12483th slice voxelvolume 3.1901 mm3 Loading mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii Search region is 84788 voxels = 270482.522603 mm3 Polynomial detrending, order = 0 Detrending Cannot allocate memory I am using the binaries from "freesurfer-Linux-rh9-stable-pub-v4.0.5". I am pretty new to FSFAST. Any pointers will be helpful. regards, Krishna

2 3

preprocessing error
by jake＠nmr.mgh.harvard.edu 27 Jan '09

27 Jan '09

Hi, I am attempting to run the following command: preproc-sess -s CD_R01BTX_ctrl1_sess1 -df sessdirfile -mcout fmc5 -fwhm 5 -smin fmc5 -smout fmcsm5 and am getting an error: >>>Tue Jan 27 16:33:44 EST 2009 >>>mcparams2exterg: finished >>>\n\n >>>Tue Jan 27 16:33:44 EST 2009 >>>mc-sess completed SUCCESSFULLY >>>CD_R01BTX_ctrl1_sess1 Smooth ------------------------ >>>Tue Jan 27 16:33:44 EST 2009 >>>/autofs/space/amaebi_035/users/ablood/R01_Botox >>>spatialsmooth-sess -i fmc5 -o fmcsm5 -fwhm 5 -fsd bold -umask 2 -s >>>CD_R01BTX_ctrl1_sess1 -d /autofs/space/amaebi_035/users/ablood/R01_Botox >>>---------------------------------------- >>>------------------------------------------------ >>>------------------------------------------------ >>>/autofs/space/amaebi_035/users/ablood/R01_Botox/CD_R01BTX_ctrl1_sess1 >>>Tue Jan 27 16:33:45 EST 2009 >>>/autofs/space/amaebi_035/users/ablood/R01_Botox/CD_R01BTX_ctrl1_sess1/bold >>>/space/amaebi/35/users/ablood/R01_Botox >>>RunList 016 017 018 019 020 021 >>>---------------------------------------------- >>>/autofs/space/amaebi_035/users/ablood/R01_Botox/CD_R01BTX_ctrl1_sess1/bold >>>ipfsl -i 016/fmc5 -o 016/fmcsm5 -pct .1 -fwhm 5 -fmt bhdr >>>---------------------------------------------- >>>ERROR: cannot find /usr/pubsw/packages/fsl/4.1.2/bin/ip >>>ERROR: ipfsl failed >>>ERROR: spatialsmooth-sess failed Can anyone tell me what I am doing wrong? thanks!! Jake Bugr FREESURFER_HOME: /usr/local/freesurfer/stable3 >>>we have to use stable3 for specific reasons Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/amaebi/35/users/ablood/R01_Botox PWD: /space/amaebi/35/users/ablood/R01_Botox

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Re: [Freesurfer] possible memory allocation problem - make_average_volume
by Douglas N Greve 27 Jan '09

27 Jan '09

I don't think you'll need to run the surfaces again. --no-aseg is passed to make_average_volume from make_average_subject. Ruchika Shaurya Prakash wrote: > I just downloaded the latest version last week. Is there a change since then? > Also, I get the --no-aseg option with make_average_volume and not with > make_average_subject - but I am thinking that is probably okay since the > surfaces are already done. Do you think that I need to run the surfaces again? > > Thanks, > -Ruchika. > > > ---- Original message ---- > >> Date: Tue, 27 Jan 2009 15:01:20 -0500 >> From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] possible memory allocation problem - >> > make_average_volume > >> To: Ruchika Shaurya Prakash <rprakash(a)uiuc.edu> >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> >> Sorry, just run it with --no-aseg (for that you may need a new version). >> It probably ran the surfaces ok and then bonked on the volumes (and >> probably only on the aseg). >> >> doug >> >> Ruchika Shaurya Prakash wrote: >> >>> I do have this option - but that would mean that I would not get the >>> average for volumes? >>> >>> Also, if you take a look at the make_average_surface.log - that got >>> completed without any problems. So do I need to run the >>> make_average_subject command again? >>> >>> Thanks, >>> -Ruchika. >>> >>> On Jan 27, 2009, at 1:34 PM, Douglas N Greve wrote: >>> >>> >>>> Try running it with --no-vol. If you don't have this option, then you >>>> may need to upgrade. >>>> >>>> Ruchika Shaurya Prakash wrote: >>>> >>>>> Hello >>>>> >>>>> I am running the make_average script on 92 Ss and get the following >>>>> error message: >>>>> nframestat = 92 >>>>> Allocating output >>>>> mri_concat (63810) malloc: *** mmap(size=262144) failed (error >>>>> code=12) >>>>> *** error: can't allocate regions >>>>> *** set a breakpoint in malloc_error_break to debug >>>>> MRIalloc (256, 256, 256): could not allocate 262144 bytes for >>>>> 13929th slice >>>>> >>>>> >>>>> Following some of the threads, it seems like the problem is in >>>>> averaging the volumes and Doug had provided some scripts in the >>>>> following location, the link to which is not working anymore: >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> Would it be possible to put the files back? I am using freesurfer v. >>>>> 4.1.0 and am attaching the make_average_surface.log and >>>>> make_average_volume.log files, in case there are some other issues. >>>>> Thanks for your help! >>>>> >>>>> -Ruchika. >>>>> = >>>>> ---------------------------------------------------------- >>>>> > -------------- > >>>>> >>>>> ---------------------------------------------------------- >>>>> > -------------- > >>>>> ---------------------------------------------------------- >>>>> > -------------- > >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>> > > >

1 0

possible memory allocation problem - make_average_volume
by Ruchika Shaurya Prakash 27 Jan '09

27 Jan '09

Hello I am running the make_average script on 92 Ss and get the following error message: nframestat = 92 Allocating output mri_concat (63810) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate regions *** set a breakpoint in malloc_error_break to debug MRIalloc (256, 256, 256): could not allocate 262144 bytes for 13929th slice Following some of the threads, it seems like the problem is in averaging the volumes and Doug had provided some scripts in the following location, the link to which is not working anymore: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ Would it be possible to put the files back? I am using freesurfer v. 4.1.0 and am attaching the make_average_surface.log and make_average_volume.log files, in case there are some other issues. Thanks for your help! -Ruchika.

2 4

mri_volcluster question
by Dave Brohawn 27 Jan '09

27 Jan '09

Hello, Does the frame flag refer to offsets? If so, would frame 5 be the same as offset 5 (6 seconds)? Thank you, Dave Brohawn

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