Re: [Freesurfer] mri_robust_register registration file
Hi Kami, I usually use mri_convert -at nameof.lta source.mgz mapedsource.mgz it simply works (w/o the need to specify a target-template volume) because the information is stored in the lta file. mri_vol2vol should work also w/o problems. I guess we should add a --lta flag to it at some point, but --reg should work (if extension is .lta). Sadly you still need to specify the --targ template volume there. Best, Martin On Fri, 2011-07-29 at 15:07 -0400, Kami Koldewyn wrote: > Hi All, > I was trying to use the registration file that is created by > mri_robust_register with mri_vol2vol - but it is in a different format than > registration files created by bbregister or tkregister. Is it fsl format? > Is there an easy way to use this registration file with other freesurfer > functions (like mri_vol2vol)? > > Thanks very much, > > -kami > > --- > Kami Koldewyn, PhD. > McGovern Institute for Brain Research > MIT, Building 46 Room 4141 (Kanwisher Lab) > Cambridge, MA 02139 > ka...@mit.edu > > > > > > > > > ___ > 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] Error with aparcstats2table
Hi, I was trying to create a table with my statistical results (the cortical thickness and the number of vertices) and I was running: aparcstats2table --hemi lh --subjects bert NPI001 --meas thickness -t lh.aparcstas.THICKNESS.txt When I tried to also get the number of vertices a table by running: aparcstats2table --hemi lh --subjects bert NPI001 --meas vertices -t lh.aparcstas.VERTICES.txt I got the following error: aparcstats2table: error: option --measure: invalid choice: 'Voxels' (choose from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv') Why I don't have an option for the no. of vertices? Can I export from aparc.stats into a table both data: cortical thickness and no. of vertices? Many thanks, Antonella___ 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] Need help to run MRI data using Freesurfer in Mac OSx
Hi Joanna, can you send us the contents of the file transforms/talairach_avi.log? Bruce On Fri, 29 Jul 2011, joanna floria wrote: Hello Everyone, We just installed Freesurfer on Mac and the software got installed successfully. But when I am running my data, it just gets stuck in between and shows me the error. The command I used was: /Applications/freesurfer/bin/recon-all-s 002 -i /Users/kashou/Desktop/fMRI/Anesthetics/002/SPGR/MR00 -all -notal-check The error: /Applications/freesurfer/subjects/002/mri \n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin Nasser-Kashous-iMac.local 10.4.1 Darwin Kernel Version 10.4.1: Fri Jul 16 23:04:20 PDT 2010; root:xnu-1504.7.51~1/RELEASE_I386 i386 recon-all -s 002 exited with ERRORS Can anyone please help me out with the error? Thanks, Joanna ___ 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] Need help to run MRI data using Freesurfer in Mac OSx
Hello Everyone, We just installed Freesurfer on Mac and the software got installed successfully. But when I am running my data, it just gets stuck in between and shows me the error. The command I used was: /Applications/freesurfer/bin/recon-all-s 002 -i /Users/kashou/Desktop/fMRI/Anesthetics/002/SPGR/MR00 -all -notal-check The error: /Applications/freesurfer/subjects/002/mri \n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin Nasser-Kashous-iMac.local 10.4.1 Darwin Kernel Version 10.4.1: Fri Jul 16 23:04:20 PDT 2010; root:xnu-1504.7.51~1/RELEASE_I386 i386 recon-all -s 002 exited with ERRORS Can anyone please help me out with the error? Thanks, Joanna ___ 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] Error with aparcstats2table
Hi Antonella, what do you mean by no. of vertices? The total # in the surface? You can get that with mri_info. It's loosely related to surface area, but not that interested a quantity. Bruce On Fri, 29 Jul 2011, Antonella Kis wrote: Hello everyone, I was trying to create a table with my statistical results (the cortical thickness and the number of vertices) and I was running: aparcstats2table --hemi lh --subjects bert NPI001 --meas thickness -t lh.aparcstas.THICKNESS.txt When I tried to also get the number of vertices a table by running: aparcstats2table --hemi lh --subjects bert NPI001 --meas vertices -t lh.aparcstas.VERTICES.txt I got the following error: aparcstats2table: error: option --measure: invalid choice: 'Voxels' (choose from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv') I Why I don't have an option for the no. of vertices? Can I get a table with both data: cortical thickness and no. of vertices? Many thanks, Antonella ___ 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] mri_robust_register registration file
Hi Kami mri_robust_register should create .lta files (linear transform arrays, although in practice they are almost always just single linear transforms), which is our preferred xform file format as it has all the necessary info to figure out coordinate systems and such. The current version of vol2vol (and in fact anything that reads a register.dat) should be able to read it fine, just make sure the extension is .lta so things know what format it is. cheers Bruce On Fri, 29 Jul 2011, Kami Koldewyn wrote: > Hi All, > I was trying to use the registration file that is created by > mri_robust_register with mri_vol2vol - but it is in a different format than > registration files created by bbregister or tkregister. Is it fsl format? > Is there an easy way to use this registration file with other freesurfer > functions (like mri_vol2vol)? > > Thanks very much, > > -kami > > --- > Kami Koldewyn, PhD. > McGovern Institute for Brain Research > MIT, Building 46 Room 4141 (Kanwisher Lab) > Cambridge, MA 02139 > ka...@mit.edu > > > > > > > > > ___ > 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] mri_robust_register registration file
Hi All, I was trying to use the registration file that is created by mri_robust_register with mri_vol2vol - but it is in a different format than registration files created by bbregister or tkregister. Is it fsl format? Is there an easy way to use this registration file with other freesurfer functions (like mri_vol2vol)? Thanks very much, -kami --- Kami Koldewyn, PhD. McGovern Institute for Brain Research MIT, Building 46 Room 4141 (Kanwisher Lab) Cambridge, MA 02139 ka...@mit.edu ___ 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] Error with aparcstats2table
Hello everyone, I was trying to create a table with my statistical results (the cortical thickness and the number of vertices) and I was running: aparcstats2table --hemi lh --subjects bert NPI001 --meas thickness -t lh.aparcstas.THICKNESS.txt When I tried to also get the number of vertices a table by running: aparcstats2table --hemi lh --subjects bert NPI001 --meas vertices -t lh.aparcstas.VERTICES.txt I got the following error: aparcstats2table: error: option --measure: invalid choice: 'Voxels' (choose from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv') I Why I don't have an option for the no. of vertices? Can I get a table with both data: cortical thickness and no. of vertices? Many thanks, Antonella___ 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] Intensity Normalization error
Hi Antonella, I'll leave 2) for others. For 1), it's only worth intervening/adding control points if the white surface doesn't extend all the way out to the end of a white matter strand (or if the gray matter over it doesn't get all the way out either) cheers Bruce On Fri, 29 Jul 2011, Antonella Kis wrote: > Dear Bruce, > > 1). What is the minimum value/the range for the intensity in order to be > considered acceptable? I know the value in wm should be very close to > 110 but what is the accepted value closed to this? > If is not exactly 110 (foe example if is 101) do I need to add control points > in order to normalize the intensity and get the value 110? > > 2). I was trying to create a table with my statistical results (the cortical > thickness and the number of vertices) and I was running: > > aparcstats2table --hemi lh --subjects bert NPI001 --meas thickness -t > lh.aparcstas.THICKNESS.txt > > When I tried to also get the number of vertices a table by running: > aparcstats2table --hemi lh --subjects bert NPI001 --meas vertices -t > lh.aparcstas.VERTICES.txt I got the following error: > > aparcstats2table: error: option --measure: invalid choice: 'Voxels' (choose > from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv') > > I Why I don't have an option for the no. of vertices? > Can I get a table with both data: cortical thickness and no. of vertices? > > Many thanks, > Antonella > > ___ 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] Intensity Normalization error
Dear Bruce, 1). What is the minimum value/the range for the intensity in order to be considered acceptable? I know the value in wm should be very close to 110 but what is the accepted value closed to this? If is not exactly 110 (foe example if is 101) do I need to add control points in order to normalize the intensity and get the value 110? 2). I was trying to create a table with my statistical results (the cortical thickness and the number of vertices) and I was running: aparcstats2table --hemi lh --subjects bert NPI001 --meas thickness -t lh.aparcstas.THICKNESS.txt When I tried to also get the number of vertices a table by running: aparcstats2table --hemi lh --subjects bert NPI001 --meas vertices -t lh.aparcstas.VERTICES.txt I got the following error: aparcstats2table: error: option --measure: invalid choice: 'Voxels' (choose from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv') I Why I don't have an option for the no. of vertices? Can I get a table with both data: cortical thickness and no. of vertices? Many thanks, Antonella ___ 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] isxconcat-sess missing dof file
Hi all, When I run isxconcat-sess, I am experiencing an error finding a 'dof' file in my analysis directories within the FSD files. subjects directory: /cluster/manoach/milton/subjects command line: isxconcat-sess -sf sessid_all -analysis mstmct_v_base -c type_v_rest_vol -o /cluster/manoach/milton/subjects/group_analysis/volume/ output: /cluster/manoach/milton/subjects/group_analysis/volume//mstmct_v_base/log/isxconcat.log ERROR: cannot find /autofs/cluster/manoach/milton/subjects/PAMST02/bold/mstmct_v_base/dof Did I miss a step before the isxconcat? Thank you! ___ 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] Problems at mri_em_register
Hi Tali did you check the skull stripping to make sure it didn't fail? Bruce On Fri, 29 Jul 2011, Tali Swisher wrote: Hi all, I'm running FreeSurfer v4.0.5 and keep getting the following error: ### #- #@# EM Registration Thu Jul 28 16:09:51 EDT 2011 /home/pnlstaff/freesurfer/subjects/ucsd_20110726/mri mri_em_register -mask brainmask.mgz nu.mgz /share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) spacing=8, using 2185 sample points, tol=1.00e-05... register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=29.0 using (130, 118, 99) as brain centroid... mean wm in atlas = 107, using box (130,93,92) --> (129, 143,105) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Linux compute-4-7.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Jul 28 16:11:08 EDT 2011 Any ideas? Thanks! -- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150 ___ 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] Problems at mri_em_register
Hi all, I'm running FreeSurfer v4.0.5 and keep getting the following error: ### #- #@# EM Registration Thu Jul 28 16:09:51 EDT 2011 /home/pnlstaff/freesurfer/subjects/ucsd_20110726/mri mri_em_register -mask brainmask.mgz nu.mgz /share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) spacing=8, using 2185 sample points, tol=1.00e-05... register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=29.0 using (130, 118, 99) as brain centroid... mean wm in atlas = 107, using box (130,93,92) --> (129, 143,105) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Linux compute-4-7.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Jul 28 16:11:08 EDT 2011 Any ideas? Thanks! -- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150 ___ 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] trac-all -path errors
Hi Ping,
The text files get created in the trac-all -prior stage. Maybe something
went wrong in that step. Is this the case for all the tracts or just for
this tract? If you can send us the trac-all.log file under the scripts
directory it'll be easier to troubleshoot as to what went wrong.
-Priti
> Hi,
>
> I got the error running "trac-all -path -c configure.txt"
>
> ERROR: Could not open
> ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt
>
>
> I can only find only image files in the "dlabel/diff" directory, but
> not text files.
>
> Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file?
>
> Thanks,
>
> Ping
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] trac-all -path errors
Hi,
I got the error running "trac-all -path -c configure.txt"
ERROR: Could not open
${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt
I can only find only image files in the "dlabel/diff" directory, but
not text files.
Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file?
Thanks,
Ping
___
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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
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Re: [Freesurfer] mris_expand not expanding
Hi Reza, what version are you running, and what is your command line? In the current version, this works for me: mris_expand -n 11 -thickness \ /homes/4/fischl/local_subjects/bruce/surf/lh.white 1 \ /homes/4/fischl/local_subjects/bruce/surf/lh.mid \ this will create surfaces named lh.mid001 through lh.mid011 cheers Bruce On Fri, 29 Jul 2011, Reza Farivar wrote: > Hello, > > I've tried running mris_expand on several different surfaces, with or > without the -thickness flag, and while it ends without error and creates > the output file, the output looks identical to the input. I've tried even > expanding by large amounts, large percentages of thickness values, but > without luck. Are there some hidden flags that I should be using? > > Thanks, > > Reza > ___ > 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] 20% changes
Ji Jessica, that's pretty low contrast. I would also bet that it's low bandwidth and hence you have big temporal lobe B0 distortions that will change with subject positioning. Are you stuck with this data going forward, or can you change the acquisition parameters? If not, I think you will have to live with lower reliability and sensitivity cheers Bruce On Thu, 28 Jul 2011, Jessica Liu wrote: Hi Bruce, I was thinking it could be quality as well, since I asked about that in a previous question where my group compared 3T and 1.5T data from the same subject. Unfortunately we only obtained 1 scan for all of our subjects and nearly all of our data is from a 1.5T scanner. I've attached coronal, axial, and sagittal views with aseg+aparc, and one image without aseg+aparc for a WM segmentation check. Thanks for your help! Jessica On Thu, Jul 28, 2011 at 11:39 AM, Bruce Fischl wrote: Hi Jessica the problem may be data quality! At 1.5T with a volume coil we would typically get 2 scans to average. A TR of 14 is pretty short and will reduce the SNR, and a TE of 6 is quite long and will reduce contrast. Can you send us a tif of one slice to look at? Bruce On Thu, 28 Jul 2011, Jessica Liu wrote: Hi Martin, When I did longitudinal analyses in the past, the output was very strange even though I think I did everything correctly. If it's not too much trouble for you, could you please take a look at my data and tell me what I've done wrong? Since the files are so large, how would I send over my data? Also, I'm using is a head coil 1.5T single-channel GE scanner. The sequence I'm using is 3D SPGR with TR = 14 msec, TE = 6.2 msec, TI = 450.0, FOV 24 cm, data acquisition matrix = 256x192, and 124 slices with 1.6 mm thickness. Your help is truly appreciated! Jessica On Thu, Jul 28, 2011 at 7:37 AM, Martin Reuter wrote: Hi Jessica, I'd recommend to run the -base and the -long on these and see what happens. If you then still see these differences, maybe we can take a look at your data to figure out what causes this. It could be that the WM segmentation fails somewhere. Anyway, the longitudinal stream should help fix these things. Are these mprages or multi echo mprages? 3T? what coil? Best, Martin On Wed, 2011-07-27 at 18:01 -0700, Jessica Liu wrote: > Hi Bruce, > > Well for one of the subjects, the total temporal lobe volume from the > first scan was 149937 mm3, and the second scan's total temporal lobe > volume was 183121 mm3. These numbers were found by summing the > volumes from the entorhinal, fusiform, parahippocampal, temporal pole, > transverse temporal, and the inferior, middle, and superior temporal > sections found in the lh.aparc.stats, rh.aparc.stats, and wmparc.stats > for the respective scans. Hippocampus volumes were found by summing > the right and left parts found in aseg.stats. > > Jessica > > On Wed, Jul 27, 2011 at 5:37 PM, Bruce Fischl > wrote: > how are you computing the 20% difference? We definitely don't > see this, and Martin has done extensive testing of > repeatability. > Bruce > > > > On Wed, 27 Jul 2011, Jessica Liu wrote: > > Hi Martin, > > Thanks for getting back to me. Actually I have two > young controls who have 20% differences between two > scans a day apart. Visually, there > are not abnormalities for the surfaces and hippocampus > in both subjects i.e. on tkmedit, the color of the > hippocampus area (yellow) looks > alright to me. I don't see any motion artifacts > either. > > Jessica > > On Wed, Jul 27, 2011 at 12:15 PM, Martin Reuter > wrote: > Hi Jessica, > > I don't think this is normal. Is this a single > subject? Of course in a > single subject lots of stuff can go wrong. Are > the surfaces correct? And > the hippo label? Are there motion artifacts in > the image etc. > > Anyway, you should process this with the > longitudinal stream: > > http://freesurfer.net/fswiki/LongitudinalProcessing > which should increase repeatability. > > Best, Martin > > >
Re: [Freesurfer] Defining an mrs voxel in the anatomical dataset for partial volume correction
Hello! About synthesising a volume using mri_volsynth with direction cosines and RAS from mrs header: In the mrs header I have: - VOI position in the 3 views (sag, cor and tra) which are from the left upper corner of the voxel (these are the RAS coordinates that I need to feed into mri_volsynth, correct?) - position vectors [0] [1] [2] - row and columns vectors (but I think that these are not the ones used to get the direction cosines, is that right?) - VOIRotationInPlane - and I know that my voxel is 3x3x3 cm How do I introduce these infos in mri_volsynth to have a 3x3x3 cube to coregister with the anatomical? Typing mri_volsynth --help I got lots of asked information and I don't know how to feed it into. Also, for defining the geometry the "center" voxel and the first voxel are needed. Shouldn't it be only the RAS of the corner of the voxel? Also, all these infos are in the scanner space, and the anatomical image processed in FS is spacially transformed. What should I use to coregister the synthesized volume to the processed anatomical to get the same transformation in the 3x3x3 volume? Can you give me an example of how this process is done? Thank you very much! Andreia > Hi Doug, > > Ok. Thank you! :) > > Andreia > > Citando Douglas N Greve : > >> Yes, that should work. You will need a registration matrix to give to >> mri_compute_volume_fractions. You can get this from tkregister2: >> >> tkregister2 --mov mrs.vol.nii --s subject --regheader --reg register.dat >> >> when you run this, hit the compare button to make sure that the mrs box >> falls on the part of the anatomical you think it should be. Then hit >> "Save" to save the registration. >> >> doug >> >> _andre...@sapo.pt wrote: >>> Hi Doug, >>> >>> This already sheds some light on the issue! I didn't know >>> mri_volsynth, I'm a begginer in FS. Lets see if I got it right. I have >>> the anatomical and the MRS data acquired in the same session, so I >>> won't need the EPI. If I manage to create the MRS volume using the >>> header info and mri_volsynth I only need to coregister my anatomical >>> with the synthetised volume and then run mri_compute_volume_fractions >>> through the synthesed volume and the identity matrix (?) (since my >>> data are from the same session) to get the % of the different tissue >>> types only inside the voxel. Of course I'll need more advice on this >>> later, but one thing at a time. >>> >>> Thanks! >>> Andreia >>> >>> >>> >>> Citando Douglas N Greve : >>> Sorry, I don't know anyone who can help with that. As you note, people do it, so there must be people around who can extract the relevant information out of the header. The information you need are the direction cosines and RAS of the corner of the voxel. You can feed this into mri_volsynth. To register to FS, you'll need to have a whole-brain volume collected during the same session. If you collected the anatomical analyzed in FS at the same time, then you don't need another. If you did not, you can literally use any whole brain acquisition, eg, a single TR of an EPI (less than 10 sec to acquire). You can then register the EPI to the anatomical with bbregister. This gives you a "register.dat". You can then concatenate that with the EPI-MRS registration (I can show you how). After that, you can run mri_compute_volume_fractions passing it the synthesized volume and the register.dat (or identity matrix if same session). Another alternative is to collect an actual MRI volume that spans your MRS volume. You can then substitute that for the synthetic volume. Note that the actual pixel content of this volume is irrelevant -- it's just used to get geometry information out of it. This will be the easiest if you can do it. doug _andre...@sapo.pt wrote: > Hi Doug, > > Do you know who can help me with this? That's exactly what I think > that I need to do... The thing is that, unfortunately, I can't find > anyone who can describe how the creation of an MRI "volume" from the > MRS voxel is done, although this approach is present in many many > papers. > > About the second part, how do I register the synthetized MRI "volume" > to the FS anatomical? And how can I get the volumes of only that > "volume"? > > (Hopefully I'll find a way to do the first part...) > > Thanks, > Andreia > > > > > Citando Douglas N Greve : > >> Hi Andreia, I've done this before using information in the >> spectroscopy >> header, then synthesizing an MRI "volume" with one voxel that >> covers the >> size of your spectroscopy voxel, then registering that to the FS >> anatomical, then computing the partial volume fractions from the >> anatomical. The hard part is the first step, which I can't really >> advise >> you on. >>
[Freesurfer] mris_expand not expanding
Hello, I've tried running mris_expand on several different surfaces, with or without the -thickness flag, and while it ends without error and creates the output file, the output looks identical to the input. I've tried even expanding by large amounts, large percentages of thickness values, but without luck. Are there some hidden flags that I should be using? Thanks, Reza ___ 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] script to calculate global cortical thickness, volume etc, Is there any better way
Dear Sir/Madame
I have written a script that calculates the cortical thickness for the
whole hemisphere of the brain. I have some question if there are any
ways to improve the script. I can quite easily write a script in Python
that runs through the file I have created and append it to a coma
separate file. What is the standard way to get average cortical
thickness for the entire brain using ?h.cortex.label for serval
different subjects?
Your faithfully
Knut J
#!/bin/sh
subjects=""
for filename in ${subjects}; do
echo "subject ${filename}"
mris_anatomical_stats -f rh_${filename}.txt ${filename} rh
mris_anatomical_stats -f lh_${filename}.txt ${filename} lh
done
___
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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.
