[Freesurfer] cannot allocate memory problem when using make average subject
Hi, I was trying to build an average subject using 250 subjects and I got the following error message: processing subject nor76 (246 of 250) reading spherical surface /DATA_FREESURFER/Data/nor76/surf/rh.sphere.reg... reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) curvature mean = -0.017, std = 0.597 curvature mean = -0.064, std = 0.640 ripping medial wall... computing parameterization for surface /DATA_FREESURFER/Data/nor76/surf/rh.inflated.H... ImageAlloc: could not allocate 512x256 buffer curvature mean = -0.088, std = 0.872 Cannot allocate memory I saw someone discussing this issue a few month ago and Doug provided new scripts of make_average_subject, make_average_volume and make_average_surface to solve this problem. However, I can't find these files using the link ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ Can anyone tell me whether and how this problem has been solved? Thanks in advance! Jiefeng Jiang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Possible to regress whole-brain functional data against continuous variables in the volume?
Hi FreeSurfers. Is it possible to regress functional data against a continuous variable in the volume? I'm analyzing a reward processing study that activates sub-cortical and cortical regions, and I'd like to regress those data against a continuous measure of depressive symptoms administered to each participant. I understand the basic fsgd/mri_glmfit approach from the FS tutorial, but I want to stay in the volume in order to examine sub-cortical structures (e.g., nucleus accumbens). Is this possible? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ipfsl failed
Hello, I received the following error: (csh executable, ran from /autofs/homes/014/jake/AnalysisPrograms/CD_DMRFASL_ctrl2_ContrastAnalysis.csh) /autofs/space/amaebi_035/users/ablood/DMRF_ASL/CD_DMRFASL_ctrl2 Mon May 19 10:16:02 EDT 2008 /autofs/space/amaebi_035/users/ablood/DMRF_ASL/CD_DMRFASL_ctrl2/bold /space/amaebi/35/users/ablood/DMRF_ASL RunList 019 020 021 022 023 024 -- /autofs/space/amaebi_035/users/ablood/DMRF_ASL/CD_DMRFASL_ctrl2/bold ipfsl -i 019/fmc4 -o 019/fmcsm4 -pct .1 -fwhm 4 -fmt bhdr -- ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip ERROR: ipfsl failed ERROR: spatialsmooth-sess failed bugr: REESURFER_HOME: /usr/local/freesurfer/stable3 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/sake/3/users/inverse/subjects (looking at logfile, for the command dir is /space/amaebi/35/users/ablood/DMRF_ASL.) PWD: /space/amaebi/35/users/ablood/DMRF_ASL/log (logfile in log directory is preproc-CD_DMRFASL_ctrl2-bold.log) If anyone can help me, (im new to this) I would greatly appreciate it. Thank you in advance, Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ipfsl failed
Why are you using stable3? If that's what you really want, then you need to use version 3 of FSL, eg /usr/pubsw/packages/fsl/3.3.7 doug [EMAIL PROTECTED] wrote: Hello, I received the following error: (csh executable, ran from /autofs/homes/014/jake/AnalysisPrograms/CD_DMRFASL_ctrl2_ContrastAnalysis.csh) /autofs/space/amaebi_035/users/ablood/DMRF_ASL/CD_DMRFASL_ctrl2 Mon May 19 10:16:02 EDT 2008 /autofs/space/amaebi_035/users/ablood/DMRF_ASL/CD_DMRFASL_ctrl2/bold /space/amaebi/35/users/ablood/DMRF_ASL RunList 019 020 021 022 023 024 -- /autofs/space/amaebi_035/users/ablood/DMRF_ASL/CD_DMRFASL_ctrl2/bold ipfsl -i 019/fmc4 -o 019/fmcsm4 -pct .1 -fwhm 4 -fmt bhdr -- ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip ERROR: ipfsl failed ERROR: spatialsmooth-sess failed bugr: REESURFER_HOME: /usr/local/freesurfer/stable3 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/sake/3/users/inverse/subjects (looking at logfile, for the command dir is /space/amaebi/35/users/ablood/DMRF_ASL.) PWD: /space/amaebi/35/users/ablood/DMRF_ASL/log (logfile in log directory is preproc-CD_DMRFASL_ctrl2-bold.log) If anyone can help me, (im new to this) I would greatly appreciate it. Thank you in advance, Jake ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Question regarding computing contrasts with mri_glmfit
All, I'm just looking for a little advice on constructing fsgd and .mat files. I would like to compare a healthy control sample with the data from two MDD groups. To do so I made my fsgd file to look like the following: GroupDescriptorFile 1 Title MoneyGame_Subjects Class Control Class MDD Class Anhedonic Input REWARD111 Control Input REWARD201 Anhedonic Input REWARD207 MDD Input REWARD208 Anhedonic Input REWARD211 MDD Input REWARD212 MDD Input REWARD213 Anhedonic Input REWARD215 Anhedonic Input REWARD277 Control Input REWARD278 Control This file results in a design matrix with 3 columns. I am interested in conducting the following analyses and I wanted to check to see if I am coding all of the .mat files correctly. Controls vs all Patients (1 -.5 -.5) Anhedonic vs MDD (0 1 -1) Controls vs Anhedonic (1 0 -1) Controls vs MDD (1 -1 0) Thank you in advance for any help you can offer. Avram -- Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Porting Freesurfer data
Hi Freesurfer gurus experts, I'm trying to port Freesurfer data into an Afni-compatible format. I have some questions regarding this process - 1. I came up with the idea of converting Freesurfer data to the Analyze format (from the PDF on the FSWiki), and then to Afni. I'm not exactly sure how to create Analyze's .img files, as there doesn't seem to be any documentation on this. Is there a way to do this, or am I heading down an overly complicated route? Is there a better way to convert Freesurfer data into Afni's format? 2. Given .mgz files, I tried gunzip-ing them, but received an error saying that the extension was an unknown format. How do I unzip these files? I'd really appreciate any help you can give me. Thanks, Navaneethan -- Navaneethan Santhanam Department of Computer Science University of Illinois at Urbana-Champaign Contact - 1-217-714-6954 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Porting Freesurfer data
Hi Navaneethan, mri_convert file.mgz file.img should convert to analyze (or you can use the .nii output extension to convert to Nifti instead, which is probably a better choice). cheers, Bruce On Mon, 19 May 2008, Navaneethan Santhanam wrote: Hi Freesurfer gurus experts, I'm trying to port Freesurfer data into an Afni-compatible format. I have some questions regarding this process - 1. I came up with the idea of converting Freesurfer data to the Analyze format (from the PDF on the FSWiki), and then to Afni. I'm not exactly sure how to create Analyze's .img files, as there doesn't seem to be any documentation on this. Is there a way to do this, or am I heading down an overly complicated route? Is there a better way to convert Freesurfer data into Afni's format? 2. Given .mgz files, I tried gunzip-ing them, but received an error saying that the extension was an unknown format. How do I unzip these files? I'd really appreciate any help you can give me. Thanks, Navaneethan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Porting Freesurfer data
Navaneethan, To answer #2, .mgz is indeed gzipped .mgh but gunzip probably doesn't recognize the suffix. cp foo.mgz foo.mgh.gz gunzip foo.mgh.gz should work. -Krish On May 19, 2008, at 3:46 PM, Navaneethan Santhanam wrote: Hi Freesurfer gurus experts, I'm trying to port Freesurfer data into an Afni-compatible format. I have some questions regarding this process - 1. I came up with the idea of converting Freesurfer data to the Analyze format (from the PDF on the FSWiki), and then to Afni. I'm not exactly sure how to create Analyze's .img files, as there doesn't seem to be any documentation on this. Is there a way to do this, or am I heading down an overly complicated route? Is there a better way to convert Freesurfer data into Afni's format? 2. Given .mgz files, I tried gunzip-ing them, but received an error saying that the extension was an unknown format. How do I unzip these files? I'd really appreciate any help you can give me. Thanks, Navaneethan -- Navaneethan Santhanam Department of Computer Science University of Illinois at Urbana-Champaign Contact - 1-217-714-6954 ___ 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
