Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Version 4.5.0 update question
by Jesse Bledsoe 26 Jul '10

26 Jul '10

Hi everyone, We are currently running version 4.2 and will be updating to version 4.5. I have about 60 brains that went through reconstruction with 4.2 and was wondering if the reconstructions/data will be affected at all by updating to 4.5? Will I need to re-run part of recon-all in order to use the updated Destrieux atlas? Thank you for your time, Jesse -- Jesse Bledsoe, M.A. Clinical Psychology Graduate Student Assistant Director, Consortium for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.

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spmregister-sess error
by Adam Nitenson 26 Jul '10

26 Jul '10

Hello Freesurfers, I am in the process of unpacking scan data, but am having problems with the spmregister-sess command. I ran recon-all and preproc-sess to completion without error. However, when I run "spmregister-sess -s FB0011090BB", I receive the following error: ">> >> >> ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg" I have unpacked several other subjects before using these same commands without issues. Why might I be receiving this error now? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

2 1

Segmentation fault at mri_ca_register
by MacDonald, Christine 26 Jul '10

26 Jul '10

Greetings from St. Louis. I recently installed Freesurfer version 4.5 on my Windows XP OS PC after attending your training course held at our institution, Washington University. The install went fine, and I was able to make it through all the checks in your setup and installation series on your wiki page. I attempted to then run a data set of my own and ran into the following error during autorecon2 which I have included the lines of output right before it as well: setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=766 0495: dt=0.028000, rms=0.464 (0.163%), neg=0, invalid=766 0496: dt=0.028000, rms=0.463 (0.154%), neg=0, invalid=766 0497: dt=0.024000, rms=0.463 (0.124%), neg=0, invalid=766 0498: dt=0.000438, rms=0.463 (0.002%), neg=0, invalid=766 0499: dt=0.000438, rms=0.463 (0.002%), neg=0, invalid=766 0500: dt=0.000219, rms=0.463 (0.001%), neg=0, invalid=766 0501: dt=0.000014, rms=0.463 (0.000%), neg=0, invalid=766 0502: dt=0.000000, rms=0.463 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.463, neg=0, invalid=766 0503: dt=0.000000, rms=0.463 (0.000%), neg=0, invalid=766 Segmentation fault ERROR: mri_ca_register with non-zero status 139 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Fri Jul 23 18:12:09 EDT 2010 /data/TB3241W/TB3241W/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Fri Jul 23 18:12:10 EDT 2010 I am running with 4G of RAM and a quad-core processor. At first I thought it was because of the 2GB max space limit in VMware so I even built and mounted a 100GB drive internal to VMware and ran all the data from there. Additionally when I check the disk space after this error it shows it only used ~1% of the 100GB mounted disk in VMware so I know I have room. Output from typing 'bugr' per your request on wiki is the following: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 Debian version: 5.0 Kernel info: Linux 2.6.28-11-generic i686 Any thoughts or guidance as to what may be going wrong? I fully admit to my novice status with Freesufer and kindly look forward to any and all advice. I found one reference to a similar problem searching through your Freesurfer support Old Archive but the response from your organization was just a further inquiry for additional information so I was unsure as to how to proceed. Thank you in advance for the help! Best Regards, Christine Mac Donald Washington University Saint Louis, MO

2 1

Siemens Trio 3T imaging parameters
by Tricia Merkley 25 Jul '10

25 Jul '10

Hi Freesurfers, Does anyone have a suggestion for an optimal scanner protocol for structural scans using Siemens Trio 3T? Thanks, Tricia Merkley

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problems visualizing in tksurfer
by Michael Scheel 25 Jul '10

25 Jul '10

Hi fs-experts, I want to visualize thickness files and am succesful as long I use the Heat LUT. When I use the RedGreen Overlay for some reason the Overlay is visualized purple. Any ideas why that is? I'm running FS 4.5 on a Mabook Pro. Is there a Rainbow-Color LUT to download somewhere? Thanks, Michael s

1 0

error in mri_label2vol
by Mario Ortega 23 Jul '10

23 Jul '10

Hi freesurfer programmers, I have a specific question reagrding the output of mri_label2vol. The image is correctly converted, however the analyze header file has an orientation value set to -1. This is invalid as analyze orient fields can only be 0-5, and my next scripts rely on the orient string to perform transformations. See - http://eeg.sourceforge.net/mri_orientation_notes.html Should I manually edit the orient field in the header? or does -1 field = analyze 4? Thanks, Mario Ortega Here is my specific command line output. running the command: *mri_label2vol --seg aparc+aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg. img --regheader aparc+aseg.mgz* /mnt/data/freesurfer Number of labels: 0 Annot File: (null) Template Volume: rawavg.mgz Outut Volume: aseg-in-rawavg.img Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 $Id: mri_label2vol.c,v 1.25.2.4 2009/07/08 16:28:40 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 128.000; -0.000 1.000 -0.000 88.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Computing registration based on header RegMat: -------- 0.019 0.998 -0.052 0.000; -0.999 0.021 0.035 0.000; 0.036 0.052 0.998 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -0.019 -0.998 0.052 128.000; -0.036 -0.052 -0.998 128.000; -0.999 0.021 0.035 88.000; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT ASeg2Vol: Sorting ASeg2Vol: Mapping ASeg2Vol: Reverse Map nmisses = 342870 (46013 filled) ASeg2Vol: done Analyze Output Matrix -0.019 -0.036 -0.999 98.696; -0.998 -0.052 0.021 164.924; 0.052 -0.998 0.035 115.862; 0.000 0.000 0.000 1.000; -------------------- *INFO: set hdr.hist.orient to -1* /mnt/data/freesurfer Number of labels: 0 Annot File: (null) Template Volume: rawavg.mgz Outut Volume: aseg-in-rawavg.img Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0

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30 gigabyte recon-all.log file after protocol error
by Max Gunther 23 Jul '10

23 Jul '10

Dear FreeSurfers, I am new to FreeSurfer and just trying to run some simple volumetric analysis and I get a "Protocol error". I went to look at the log file and it is 30 gigabytes in size so something is going awry here... Is there a way to break this error down further to understand what may be going wrong? I am running FreeSurfer in the Oracle virtual machine. The command that I am running after I set up the environment and convert the file structure is recon-all -s TED -all. Then I tried recon-all -s TED -autorecon1 I have tried this on a couple of different subjects and have tried deleting and cleaning up the directories and remaking them, checking to make sure that I have enough hard drive space etc., but I keep getting the same error messages. Below are the error messages that I am receiving. Thanks for you time. Sincerely, Max Max Gunther, PhD Vanderbilt University Medical Center Departments of Psychiatry and Medicine Center for Health Services Research Nashville, TN www.ICUdelirium.org freesurfer@freesurfer-virtual:/mnt$ ls 2190 Ely_2190_3_1-0001.nii Ely_2405_3_1 Ely_786_3_1 AJM Ely_2206_3_1 Ely_2409_3_1 HMN CBB Ely_2231_3_1 Ely_2448_3_1 TED Ely_1204_3_1 Ely_2290_3_1 Ely_2461_3_1 TED.nii Ely_2178_3_1 Ely_2373_3_1 Ely_783_3_1 Ely_2190_3_1 Ely_2376_3_1 Ely_783_3_1-0001.nii freesurfer@freesurfer-virtual:/mnt$ freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED.nii -force ERROR: nothing to do freesurfer@freesurfer-virtual:/mnt$ freesurfer@freesurfer-virtual:/mnt$ freesurfer@freesurfer-virtual:/mnt$ freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED -i TED.nii -force INFO: /mnt/TED exists with -i, but -force specified. Deleting any previous source volumes Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /mnt Actual FREESURFER_HOME /usr/local/freesurfer Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /mnt/TED mri_convert /mnt/TED.nii /mnt/TED/mri/orig/001.mgz mri_convert /mnt/TED.nii /mnt/TED/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /mnt/TED.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997863, 0.0653316, -0.000653581) j_ras = (0.0653335, 0.997724, -0.01666) k_ras = (0.000436332, 0.0166671, 0.999861) writing to /mnt/TED/mri/orig/001.mgz... #------------------------------------------ recon-all finished without error at Thu Jul 22 21:34:41 EDT 2010 done freesurfer@freesurfer-virtual:/mnt$ recon-all -s 2190 -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /mnt Actual FREESURFER_HOME /usr/local/freesurfer -rwxrwxrwx 1 root root 31066267445 Jul 22 21:25 /mnt/2190/scripts/recon-all.log Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux tee: /mnt/2190/scripts/recon-all.log: Protocol error #-------------------------------------------- tee: /mnt/2190/scripts/recon-all.log: Protocol error #@# MotionCor Thu Jul 22 21:36:51 EDT 2010 tee: /mnt/2190/scripts/recon-all.log: Protocol error Found 1 runs tee: /mnt/2190/scripts/recon-all.log: Protocol error /mnt/2190/mri/orig/001.mgz tee: /mnt/2190/scripts/recon-all.log: Protocol error WARNING: only one run found. This is OK, but motion tee: /mnt/2190/scripts/recon-all.log: Protocol error correction cannot be performed on one run, so I'll tee: /mnt/2190/scripts/recon-all.log: Protocol error copy the run to rawavg and continue. tee: /mnt/2190/scripts/recon-all.log: Protocol error cp /mnt/2190/mri/orig/001.mgz /mnt/2190/mri/rawavg.mgz tee: /mnt/2190/scripts/recon-all.log: Protocol error ^C freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /mnt Actual FREESURFER_HOME /usr/local/freesurfer -rwxrwxrwx 1 root root 1883387 Jul 22 21:34 /mnt/TED/scripts/recon-all.log Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux #-------------------------------------------- #@# MotionCor Thu Jul 22 21:37:17 EDT 2010 Found 1 runs /mnt/TED/mri/orig/001.mgz 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. cp /mnt/TED/mri/orig/001.mgz /mnt/TED/mri/rawavg.mgz /mnt/TED mri_convert /mnt/TED/mri/rawavg.mgz /mnt/TED/mri/orig.mgz --conform mri_convert /mnt/TED/mri/rawavg.mgz /mnt/TED/mri/orig.mgz --conform $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /mnt/TED/mri/rawavg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997863, 0.0653316, -0.000653581) j_ras = (0.0653335, 0.997724, -0.01666) k_ras = (0.000436332, 0.0166671, 0.999861) Original Data has (0.9375, 0.9375, 4.93393) mm size and (256, 256, 28) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 3 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/TED/mri/orig.mgz... mri_add_xform_to_header -c /mnt/TED/mri/transforms/talairach.xfm /mnt/TED/mri/orig.mgz /mnt/TED/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- tee: /mnt/TED/scripts/recon-all.log: Protocol error #@# Nu Intensity Correction Thu Jul 22 22:01:19 EDT 2010 tee: /mnt/TED/scripts/recon-all.log: Protocol error mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 tee: /mnt/TED/scripts/recon-all.log: Protocol error /mnt/TED/mri tee: /mnt/TED/scripts/recon-all.log: Protocol error /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.7.2.2 2009/05/04 16:16:27 nicks Exp $ Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux Thu Jul 22 22:01:20 EDT 2010 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2007-11-01 at 16:24:51 tmpdir is ./tmp.mri_nu_correct.mni.26799 /mnt/TED/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.26799/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.26799/nu0.mnc ncendef: ncid 3: Protocol error Error outputting volume: possibly disk full? $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from orig.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 4.7153e-09, -8.45737e-11) j_ras = (-3.36186e-10, -3.63052e-09, -1) k_ras = (-1.90607e-08, 1, 2.12146e-09) writing to ./tmp.mri_nu_correct.mni.26799/nu0.mnc... ERROR: mincWrite: output_volume exited with 1 ERROR: failure writing ./tmp.mri_nu_correct.mni.26799/nu0.mnc ERROR: converting to minc tee: /mnt/TED/scripts/recon-all.log: Protocol error Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux tee: /mnt/TED/scripts/recon-all.log: Protocol error recon-all exited with ERRORS at Thu Jul 22 22:01:27 EDT 2010 tee: /mnt/TED/scripts/recon-all.log: Protocol error tee: /mnt/TED/scripts/recon-all.log: Protocol error freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED -autorecon1 Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /mnt Actual FREESURFER_HOME /usr/local/freesurfer -rwxrwxrwx 1 root root 30978108369 Jul 22 22:01 /mnt/TED/scripts/recon-all.log Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux tee: /mnt/TED/scripts/recon-all.log: Protocol error #-------------------------------------------- tee: /mnt/TED/scripts/recon-all.log: Protocol error #@# MotionCor Fri Jul 23 13:02:59 EDT 2010 tee: /mnt/TED/scripts/recon-all.log: Protocol error Found 1 runs tee: /mnt/TED/scripts/recon-all.log: Protocol error /mnt/TED/mri/orig/001.mgz tee: /mnt/TED/scripts/recon-all.log: Protocol error WARNING: only one run found. This is OK, but motion tee: /mnt/TED/scripts/recon-all.log: Protocol error correction cannot be performed on one run, so I'll tee: /mnt/TED/scripts/recon-all.log: Protocol error copy the run to rawavg and continue. tee: /mnt/TED/scripts/recon-all.log: Protocol error cp /mnt/TED/mri/orig/001.mgz /mnt/TED/mri/rawavg.mgz tee: /mnt/TED/scripts/recon-all.log: Protocol error /mnt/TED tee: /mnt/TED/scripts/recon-all.log: Protocol error mri_convert /mnt/TED/mri/rawavg.mgz /mnt/TED/mri/orig.mgz --conform tee: /mnt/TED/scripts/recon-all.log: Protocol error mri_convert /mnt/TED/mri/rawavg.mgz /mnt/TED/mri/orig.mgz --conform tee: /mnt/TED/scripts/recon-all.log: Protocol error $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /mnt/TED/mri/rawavg.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997863, 0.0653316, -0.000653581) j_ras = (0.0653335, 0.997724, -0.01666) k_ras = (0.000436332, 0.0166671, 0.999861) Original Data has (0.9375, 0.9375, 4.93393) mm size and (256, 256, 28) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 3 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/TED/mri/orig.mgz... tee: /mnt/TED/scripts/recon-all.log: Protocol error Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux tee: /mnt/TED/scripts/recon-all.log: Protocol error recon-all exited with ERRORS at Fri Jul 23 13:03:10 EDT 2010 tee: /mnt/TED/scripts/recon-all.log: Protocol error tee: /mnt/TED/scripts/recon-all.log: Protocol error freesurfer@freesurfer-virtual:/mnt$ recon-all -s TED -autorecon1

1 0

Any update on releasing the source for FreeSurfer?
by Alex Waite 23 Jul '10

23 Jul '10

Hey Everyone, I searched through the archives and it seems to be that there is an intent to release FreeSurfer as open source eventually. However, the most recent post about that that I could find was from a year or two ago. Is there any update on this or plan for when this will happen? The reason why I ask is that we're looking to run FreeSurfer on Debian based systems, and it doesn't seem that you provide packages for those systems. I would be happy to compile and package this software and make it available to the community if the source was available, or made available. Thank you for your time. I look forward to hearing back from you. ---Alex

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Re: [Freesurfer] Fwd: Plotting functional data on surface
by Corey Keller 23 Jul '10

23 Jul '10

Hi Freesurfers, Thanks for all of the help so far. I just have one more quick follow-up question. Just to remind you I was attempting to plot a functional map on a pial surface in matlab. The solution was to index the functional map so that I just color-coat the pial surface accordingly instead of the usual gray. We are now trying to transform this functional data so that it will plot on the pial surface of the average subject, fsaverage. Any help will be much appreciated. Thanks again. -Corey On Fri, Jul 2, 2010 at 2:27 PM, Corey Keller <corey.j.keller(a)gmail.com> wrote: Hi, I figured out how to plot it on my pial surface. Here's my code if anyone is wondering. Thanks again for your help. In freesurfer bbregister --s CL --mov ./CL/lfo_example.nii.gz --init-fsl --reg register.dat --bold tkregister2 --mov ./CL/lfo_example.nii.gz --reg register.dat --surf mri_vol2surf --src --reg register.dat --out *.nii.gz --hemi lh In matlab mgh = MRIread('*.mgh'); surf_data = mgh.vol; iter = round((surf_data+2)*16)'; % indexing colormap map = cmap(round((surf_data+2)*16),:); tripatch(cortex.lh,h,map); shading interp; lighting gouraud; material dull; switch 'l' case 'r' l=light('Position',[1 0 0]); view(90,0) case 'ri' l=light('Position',[1 0 0]); view(90,-90) case 'l' l=light('Position',[-1 0 0]); view(270,0) case 'li' l=light('Position',[-1 0 0]); view(270,-45) end axis off, hold on On Fri, Jul 2, 2010 at 11:19 AM, Corey Keller <corey.j.keller(a)gmail.com> wrote: > Hi Freesurfers, > > I have now successfully registered the functional volume and > transformed the volume to a surface via mri_vol2surf. I then loaded > the nifti surface into matlab with MRIread (nii = > MRIread('example.nii'). nii.vol is a 1x149x797 matrix. Additionally, > there are variables of vox2ras and vox2ras1 transformation matrices in > the nii struct. Do you know how I get nii.vol into RAS coordinates and > eventually plotted? Thanks! > > Best, > Corey > > On Fri, Jul 2, 2010 at 10:06 AM, ythomas <ythomas(a)csail.mit.edu> wrote: >> Is this a preprocessed (whole brain regression, bandpass filter, etc) >> rest-state volume? If so, I would suggest using the volume before the >> preprocessing (which works well for me). >> >> Thanks, >> Thomas >> >> On Jul 2, 2010, at 9:58 AM, Corey Keller wrote: >> >>> Hi Bruce, >>> >>> Thanks for the info. I am trying to register a resting state >>> functional nifti file. I ran bbregister but it was not well aligned >>> (pictures are attached). Our thought is that the contrast was not >>> strong enough for freesurfer to detect enough common points with the >>> anatomical volume. If we feed another example >>> functional file with better contrast, could we then use that register >>> file to apply to our data? Any thoughts on how we can do this >>> betterwithout manually aligning? Thanks again. >>> >>> Best, >>> Corey >>> >>> On Fri, Jul 2, 2010 at 9:30 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>>> >>>> Hi Corey, >>>> >>>> yes, or you can try bbregister to do it automatically. >>>> >>>> cheers >>>> Bruce >>>> On Fri, 2 Jul 2010, Corey Keller wrote: >>>> >>>>> Hi Freesurfers, >>>>> >>>>> I know this is probably an easy question, but I am having some trouble >>>>> with it. I am trying to plot functional data (in nifti format) onto a >>>>> pial or inflated surface in matlab. I am uring mri_vol2surf but am >>>>> missing the register file. Do I find this from registering the >>>>> functional data to the anatomical surface via tkregister? Thanks. >>>>> >>>>> -Corey >>>>> _______________________________________________ >>>>> 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. >>>> >>>> >>> >>> <sagittal.png><Screenshot_horizontal.png>_______________________________________________ >>> 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.

2 1

functional ROI analysis for DLPFC
by Adam Nitenson 23 Jul '10

23 Jul '10

Hi all, I am trying to use func2roi-sess to analyze functional ROI data for the left and right DLPFC, but these are not listed as labels on the FreeSurferColorLUT on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurfe…. Do I need to create my own ROI labels for these? I tried the command "func2roi-sess -roidef DLPFC -analysis fmcsm5_functionals -c Cond1v7 -s FB0011046AA -maskthresh 1.3 -maskmap sig.nii " which actually ran to completion and created a DLPFC folder in my subject file, but I really have no idea if this helps at all with my goal of, to quote my PI, "look at the dorsolateral prefrontal cortex ROI data, which will generate a single value for the average activation within the right or left DLPFC for each subject, during each condition". Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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