[Freesurfer] average subject
Dear freesurfer experts, i have a question regarding making my own average. I received this message Tue Feb 12 10:54:34 GMT 2013 make_average_volume done However, the stats file in the average subject is empty, and the tmp folder, but the other folders are not empty. Is this normal? Does the above message indicate that the make_subject is done, or should it say finished without error etc. Thank you for your help, Kind Regards Linn ___ 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] preparing NHP data for whole brain analysis
Dear Freesurfer experts, I am trying to prepare some NHP functional data for a whole brain group analysis, and I was wondering which sequence of steps you would recommend, given that the data cannot be processed with recon-all. I have surfaces from 4 subjects, but one subject for which I do not have an anatomy of sufficient quality and won't be able to obtain one. I would also like to align the data to the 112RM atlas by Mclaren et al. I was thinking that I could probably align the functional data per subject to the atlas, and then use this registration with func2sph-sess to align all subjects for the group analysis (again to the atlas). Does that make sense, given that I have only four out of five individual surfaces? A second question is when to smooth the data. I assume that it makes most sense to smooth it after it has been transformed into surface space. Would that be sphsmooth-sess? Finally, when doing the analysis, I would use isxavg-re-sess or isxavg-fe- sess, correct? I am using Freesurfer v5.1. Thank you very much for your advice, Caspar ___ 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] Post-Doctoral position in brain imaging and computational morphometry – University of Geneva
Post-Doctoral applications are invited in the newly established Brain and Language Lab at the Department of Clinical Neuroscience at the University of Geneva, in collaboration with the Swiss Institute of Technology (EPFL) in Lausanne, Switzerland. Projects will include the development of new data-driven computational morphometry methods for analysis of structural magnetic resonance imaging (MRI) data, and application of these to large datasets in the context of normal variability, disease, and expertise. Candidates should have a degree in Biomedical Engineering, Computational Neuroscience, or a related field with a strong mathematical and computational background. Ideally they should have experience in brain image analysis, pattern recognition, machine learning, statistics as well as excellent programming skills. We offer a competitive starting salary of 68, 964 CHF/year, or more depending on experience. The position is available immediately, and applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (narly.golest...@unige.ch). Applications including a CV, a statement of research interests, and the names and full contact details of three referees should be sent to: narly.golest...@unige.ch. ___ 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 when using stats import in qdec
Dear all, I have a question; I am trying to load data into qdec; the data table is loaded fine (although it lists age as continuous for some region, rather than discreet). However, When i try to generate the stats table, this error comes up. Does this mean I somehow have to manually set the subjects directory to where my subjects are (rather than the default that seems to be used), using the generate stats table option? If so, how is this done? Or is it a preprocessing step I have missed out? mkdir: cannot create directory `/usr/local2/freesurfer510/subjects/qdec': Permission denied ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x30732c58): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: mkdir -p /usr/local2/freesurfer510/subjects/qdec/stats_tables/ Stack trace: Uncaught exception: command failed: mkdir -p /usr/local2/freesurfer510/subjects/qdec/stats_tables/ while executing vtkTemp2 GenerateStatsDataTables Grateful for your help Regards Catherine -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] Fwd: error when using stats import in qdec
Dear all, I have a question; I am trying to load data into qdec; the data table is loaded fine (although it lists age as continuous for some region, rather than discreet). However, When i try to generate the stats table, this error comes up. Does this mean I somehow have to manually set the subjects directory to where my subjects are (rather than the default that seems to be used), using the generate stats table option? If so, how is this done? Or is it a preprocessing step I have missed out? mkdir: cannot create directory `/usr/local2/freesurfer510/subjects/qdec': Permission denied ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x30732c58): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: mkdir -p /usr/local2/freesurfer510/subjects/qdec/stats_tables/ Stack trace: Uncaught exception: command failed: mkdir -p /usr/local2/freesurfer510/subjects/qdec/stats_tables/ while executing vtkTemp2 GenerateStatsDataTables Grateful for your help Regards Catherine -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. - End forwarded message - -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] Fwd: error when using stats import in qdec
Sorry, just to clarify; it lists age as a discreet variable rather than continuous for some reason, not the other way round as I accidentally wrote=) Regards Quoting Catherine Bois c.b...@sms.ed.ac.uk on Tue, 12 Feb 2013 14:58:45 +: Dear all, I have a question; I am trying to load data into qdec; the data table is loaded fine (although it lists age as continuous for some region, rather than discreet). However, When i try to generate the stats table, this error comes up. Does this mean I somehow have to manually set the subjects directory to where my subjects are (rather than the default that seems to be used), using the generate stats table option? If so, how is this done? Or is it a preprocessing step I have missed out? mkdir: cannot create directory `/usr/local2/freesurfer510/subjects/qdec': Permission denied ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x30732c58): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: mkdir -p /usr/local2/freesurfer510/subjects/qdec/stats_tables/ Stack trace: Uncaught exception: command failed: mkdir -p /usr/local2/freesurfer510/subjects/qdec/stats_tables/ while executing vtkTemp2 GenerateStatsDataTables Grateful for your help Regards Catherine -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. - End forwarded message - -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] Fwd: error when using stats import in qdec
Catherine, Is your SUBJECTS_DIR enviro var setup properly prior to starting qdec? That is, set to your own writable subjects directory? I noticed in the error message that it looks like the subjects dir is the default one under the /freesurfer dir, which is read-only. One option is to put this line at the top of your qdec.table.dat file: SUBJECTS_DIR /path/to/my/subjects so that you dont have to remember to set it prior to starting qdec. Also, age would be a continuous var even if its an integer, discrete is what we assign to classes like male/female or patient/control. Nick Dear all, I have a question; I am trying to load data into qdec; the data table is loaded fine (although it lists age as continuous for some region, rather than discreet). However, When i try to generate the stats table, this error comes up. Does this mean I somehow have to manually set the subjects directory to where my subjects are (rather than the default that seems to be used), using the generate stats table option? If so, how is this done? Or is it a preprocessing step I have missed out? mkdir: cannot create directory `/usr/local2/freesurfer510/subjects/qdec': Permission denied ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x30732c58): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: mkdir -p /usr/local2/freesurfer510/subjects/qdec/stats_tables/ Stack trace: Uncaught exception: command failed: mkdir -p /usr/local2/freesurfer510/subjects/qdec/stats_tables/ while executing vtkTemp2 GenerateStatsDataTables Grateful for your help Regards Catherine -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. - End forwarded message - -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] Fwd: error when using stats import in qdec
Catherine, Thats odd, can you email me your qdec.table.dat file? qdec parses 'discretes' if they're non-numerical, so maybe there is a stray character thats messing it up. Nick Sorry, just to clarify; it lists age as a discreet variable rather than continuous for some reason, not the other way round as I accidentally wrote=) Regards Quoting Catherine Bois c.b...@sms.ed.ac.uk on Tue, 12 Feb 2013 14:58:45 +: Dear all, I have a question; I am trying to load data into qdec; the data table is loaded fine (although it lists age as continuous for some region, rather than discreet). However, When i try to generate the stats table, this error comes up. Does this mean I somehow have to manually set the subjects directory to where my subjects are (rather than the default that seems to be used), using the generate stats table option? If so, how is this done? Or is it a preprocessing step I have missed out? mkdir: cannot create directory `/usr/local2/freesurfer510/subjects/qdec': Permission denied ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x30732c58): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: mkdir -p /usr/local2/freesurfer510/subjects/qdec/stats_tables/ Stack trace: Uncaught exception: command failed: mkdir -p /usr/local2/freesurfer510/subjects/qdec/stats_tables/ while executing vtkTemp2 GenerateStatsDataTables Grateful for your help Regards Catherine -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. - End forwarded message - -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] trac-all problem
hello i am trying to process the dti data with trac-all. I am new to tracula my input images are 3300 dicoms, 60 slices and 55 dti diffusions i have attached my dmrirc_single_subject file i did the following command: trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject and got the result: INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 INFO: Diffusion root is /Studies/MJMRI/MJ0012 Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Mon Feb 11 12:41:04 CST 2013 mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... Starting DICOMRead2() dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 dcmdir = /Studies/MJMRI/MJ0012//s780 Ref Series No = 13 Found 3304 files, checking for dicoms Found 3300 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 55 nslices = 60 ndcmfiles = 3300 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0016 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0017 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0018 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0019 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0020 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0021 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0022 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0023 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0024 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0025 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0026 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0027 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0028 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0029 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0030 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0031 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0032 processing
[Freesurfer] two sample t-test of paired differences
Hello, I have two different results from a paired difference analysis lets call it A and B. How can I do a two sample t-test with those results (A-B)? Somehow I am stuck in using isxconcat-sess on the group results A and B. Help is highly appreciated. Cheers Joerg ___ 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] average subject
Hi Linn that sounds normal to me cheers Bruce On Tue, 12 Feb 2013, Linn Mittlestein wrote: Dear freesurfer experts, i have a question regarding making my own average. I received this message Tue Feb 12 10:54:34 GMT 2013 make_average_volume done However, the stats file in the average subject is empty, and the tmp folder, but the other folders are not empty. Is this normal? Does the above message indicate that the make_subject is done, or should it say finished without error etc. Thank you for your help, Kind Regards Linn ___ 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] average subject
Dear Bruce, Thank you for your reply Regards, Linn On Tue, Feb 12, 2013 at 4:14 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Linn that sounds normal to me cheers Bruce On Tue, 12 Feb 2013, Linn Mittlestein wrote: Dear freesurfer experts, i have a question regarding making my own average. I received this message Tue Feb 12 10:54:34 GMT 2013 make_average_volume done However, the stats file in the average subject is empty, and the tmp folder, but the other folders are not empty. Is this normal? Does the above message indicate that the make_subject is done, or should it say finished without error etc. Thank you for your help, Kind Regards Linn 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/**compliancelinehttp://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 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] average subject
Hi Linn, make_average_subject does not compile statistics so this is normal. doug On 02/12/2013 11:14 AM, Bruce Fischl wrote: Hi Linn that sounds normal to me cheers Bruce On Tue, 12 Feb 2013, Linn Mittlestein wrote: Dear freesurfer experts, i have a question regarding making my own average. I received this message Tue Feb 12 10:54:34 GMT 2013 make_average_volume done However, the stats file in the average subject is empty, and the tmp folder, but the other folders are not empty. Is this normal? Does the above message indicate that the make_subject is done, or should it say finished without error etc. Thank you for your help, Kind Regards Linn ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Basic skullstrip Inquiry
Hi, I'm using the -gcut flag for the first time and I've noticed that the skull stripping process is still leaving small fragments of dura behind. Will this affect my surfaces? Should I manually edit the brainmask volume to remove as much of these fragments as I can? Also, should I only be concerned about the GM and cerebellum edges when checking for over-aggressive cutting, or are other brain structures important as well, e.g. optic chiasm? Thanks, --G ___ 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] two sample t-test of paired differences
Hi Joerg, see http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples and look at the 2 group with 0 covariates. doug On 02/12/2013 10:51 AM, Jörg Pfannmöller wrote: Hello, I have two different results from a paired difference analysis lets call it A and B. How can I do a two sample t-test with those results (A-B)? Somehow I am stuck in using isxconcat-sess on the group results A and B. Help is highly appreciated. Cheers Joerg ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Parallelizing on a different kind of cluster
Hi TRACULA Experts, Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm on a non-MGH cluster? Thanks! Susie Kuo ___ 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] mean cortical thickness of significant clusters in qdec
Anyone know how to reset the LOCAL? Even if temporarily to see if this is the problem? doug On 02/12/2013 08:23 AM, Richter, Julia wrote: It says the same even if I put 1.3 in quotes. :( Any other possibility to get access to the data? -Ursprüngliche Nachricht- Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Gesendet: Montag, 11. Februar 2013 19:04 An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW: AW: AW: [Freesurfer] mean cortical thickness of significant clusters in qdec It may be a German operating system replacing 1.3 with 1,3. Maybe put it in quotes, ie, 1.3 On 02/11/2013 04:17 AM, Richter, Julia wrote: Dear Doug, this is what appears when I type my command in the command window: mri_glmfit-sim --cache 1.3 abs --cwpvalthresh .99 ERROR: thresh 1,3, must be 1.3, 2.0, 3.0, 3.3, 4.0 That's it...Any ideas why this is happening? Many thanks in advance! Best, Julia -Ursprüngliche Nachricht- Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 7. Februar 2013 17:32 An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW: AW: [Freesurfer] mean cortical thickness of significant clusters in qdec it does not look like you changed the command line. Also, please cut and paste the info into the email instead of taking a snapshot. thanks doug On 02/04/2013 07:26 AM, Richter, Julia wrote: This doesn't work either (see attachment) :( -Ursprüngliche Nachricht- Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 31. Januar 2013 20:29 An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW: [Freesurfer] mean cortical thickness of significant clusters in qdec The threshold must be in the form of -log10(pthreshold). So, if you want pthreshold=.05, then use 1.3 doug On 01/31/2013 07:37 AM, Richter, Julia wrote: Dear Doug, thanks for your reply. I tried the command you suggested, but I always get an error message that there is something wrong with my threshold. I took a screenshot of the command window and attached it to this mail. I will be very happy if you have a look at it. Looking forward to your answer, Best, Julia -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve Gesendet: Mittwoch, 30. Januar 2013 17:16 An: Richter, Julia; free surfer Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in qdec Oh, sorry, I thought you said you were using mri_glmfit-sim (which does not have an FDR option). Are you using the FDR in QDEC? If so, it will display the voxel-wise threshold that realizes the FDR threshold. You can then run mri_glmfit-sim --cache threshold sign --cwpvalthresh .99 where threshold is the voxelwise threshold from FDR and sign is either abs (absolute), pos, or neg. Setting cwpvalthresh=.99 tell it to report all clusters doug On 1/30/13 8:09 AM, Richter, Julia wrote: No it is not...or I just do not find it. Might it be that I only get the xxx.y.ocn.dat if I correct for multiple comparisons with Monte Carlo? If yes, is there any possibility that I get this xxx.y.ocn.dat when correcting with FDR? Many thanks, Julia -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Dienstag, 29. Januar 2013 18:46 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in qdec Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not? doug On 01/29/2013 11:03 AM, Richter, Julia wrote: Dear FreeSurfer experts, I did a group analysis in qdec, found several significant clusters and would now like to extract the mean cortical thickness of each significant cluster. I know that I have to run mri_glmfit-sim to do this, but I do not understand which commands I need to get the xxx.y.ocn.dat as output by running mri_glmfit-sim. Any ideas? Any help is appreciated. J Best wishes, Julia ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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
Re: [Freesurfer] trac-all -path error
Hi Stefano - What are the contents of the bedpostX output directory? In your case, that'd be this directory: /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX a.y On Mon, 11 Feb 2013, std...@virgilio.it wrote: Hi list, I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I have this error: Loading mask from /Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX niiRead(): error opening file /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz From http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22066.html I'm deducing that the error may be related trace-all upload. I have doing this upload but I visualize always the same error. I attached tract-all uploades file that live in /Applications/freesurfer/bin. Please, could you check it? I have also other question. May I run the second step of trac-all (bedpostx) using FSL on other pc? In this way, could I directly run in FSL dmri folder? Do you think that I should rename some files? Thanks, Stefano ___ 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] R: trac-all -path error
Hi Stefano - There is no need to attach the trac-all script, I am quite familiar with it. Perhaps you could attach the configuration file that you set up? Thanks, a.y On Mon, 11 Feb 2013, std...@virgilio.it wrote: I'm attaching my trac-all file for check.Thanks, Stefano Messaggio originale Da: std...@virgilio.it Data: 11-feb-2013 14.42 A: freesurfer@nmr.mgh.harvard.edu Cc: ayend...@nmr.mgh.harvard.edu Ogg: [Freesurfer] trac-all -path error Hi list, I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I have this error: Loading mask from /Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX niiRead(): error opening file /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz From http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22066.html I'm deducing that the error may be related trace-all upload. I have doing this upload but I visualize always the same error. I attached tract-all uploades file that live in /Applications/freesurfer/bin. Please, could you check it? I have also other question. May I run the second step of trac-all (bedpostx) using FSL on other pc? In this way, could I directly run in FSL dmri folder? Do you think that I should rename some files? Thanks, Stefano ___ 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] preparing NHP data for whole brain analysis
Hi Caspar, with 5.1 you would not use any of those programs (ie, func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use FSFAST, then see the tutorial for getting started. You'll need to set up the directory structure properly, then run preproc-sess, mkanalysis-sess, and selxavg3-sess. For the group analysis you'll run isxconcat-sess followed by mri_glmfit and mri_glmfit-sim. If you don't have anatomicals for all subjects and you just want to use the average subject, then put the average subject into the subjectname file when you set up the directory structure. doug On 02/12/2013 07:55 AM, Caspar M. Schwiedrzik wrote: Dear Freesurfer experts, I am trying to prepare some NHP functional data for a whole brain group analysis, and I was wondering which sequence of steps you would recommend, given that the data cannot be processed with recon-all. I have surfaces from 4 subjects, but one subject for which I do not have an anatomy of sufficient quality and won't be able to obtain one. I would also like to align the data to the 112RM atlas by Mclaren et al. I was thinking that I could probably align the functional data per subject to the atlas, and then use this registration with func2sph-sess to align all subjects for the group analysis (again to the atlas). Does that make sense, given that I have only four out of five individual surfaces? A second question is when to smooth the data. I assume that it makes most sense to smooth it after it has been transformed into surface space. Would that be sphsmooth-sess? Finally, when doing the analysis, I would use isxavg-re-sess or isxavg-fe-sess, correct? I am using Freesurfer v5.1. Thank you very much for your advice, Caspar ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 problem
Hi Jon - My guess is you didn't define the nb0 variable in your configuration file, see here: http://www.freesurfer.net/fswiki/dmrirc The new version, which will come out in a few days, will be able to figure it out without you having to specify it but with the current version you have to. Hope this helps, a.y On Tue, 12 Feb 2013, Jon Wieser wrote: hello i am trying to process the dti data with trac-all. I am new to tracula my input images are 3300 dicoms, 60 slices and 55 dti diffusions i have attached my dmrirc_single_subject file i did the following command: trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject and got the result: INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 INFO: Diffusion root is /Studies/MJMRI/MJ0012 Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Mon Feb 11 12:41:04 CST 2013 mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... Starting DICOMRead2() dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 dcmdir = /Studies/MJMRI/MJ0012//s780 Ref Series No = 13 Found 3304 files, checking for dicoms Found 3300 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 55 nslices = 60 ndcmfiles = 3300 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0016 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0017 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0018 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0019 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0020 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0021 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0022 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0023 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0024 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0025 processing
Re: [Freesurfer] Parallelizing on a different kind of cluster
Hi Susie - FSL's bedpostx script works for parallelization on the type of cluster they have at Oxford, and bedpostx_seychelles is a modified version of it that also works on our cluster. Other than that, support for all possible cluster setups at other centers is beyond the scope of our research, but perhaps the existing script is useful as a starting point for making it work on your cluster. Hope this helps, a.y On Tue, 12 Feb 2013, Susan Kuo wrote: Hi TRACULA Experts, Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm on a non-MGH cluster? Thanks! Susie Kuo ___ 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] Troubleshooting the preproc
Hi Susie - avscale is part of the FSL package. You have to make sure FSL is installed and in your path. a.y On Wed, 6 Feb 2013, Susan Kuo wrote: Hi FreeSurfer community, I am currently trying to troubleshoot my preprocessing part of TRACULA with the tutorial dataset (for Diff001 as the subject, specifically), running trac-all -corr -c config dmrirc. I am running the commands in subjectID/scripts/trac-all.cmd one by one because I've had problems with some of the steps. Specifically, flip4fsl didn't work. I instead used fslswapdim -x -y z (flip4fsl uses fslswapdim x -y z, which doesn't generate the correct orientation for FSL in fact), followed by fslorient -forceradiological. I successfully ran eddy_current thereafter. Now I am stuck again, at FreeSurfer's xfmrot, which should look like: xfmrot transform file input vector file [output vector file] I specifically typed in: xfmrot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi.ecclog /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs.norot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs and received the following iterative errors: avscale: Command not found. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. Can any of you help me? Thank you, Susie K ___ 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 problem
Sorry, reading stuff from the dicom header will not work for all dicom versions. It should work for Siemens dicoms though. On Tue, 12 Feb 2013, Jon Wieser wrote: according to the http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula nb0 does not need to be specified when using original dicoms. , but i'll try defining the nb0 variable thanks Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, February 12, 2013 10:49:18 AM Subject: Re: [Freesurfer] trac-all problem Hi Jon - My guess is you didn't define the nb0 variable in your configuration file, see here: http://www.freesurfer.net/fswiki/dmrirc The new version, which will come out in a few days, will be able to figure it out without you having to specify it but with the current version you have to. Hope this helps, a.y On Tue, 12 Feb 2013, Jon Wieser wrote: hello i am trying to process the dti data with trac-all. I am new to tracula my input images are 3300 dicoms, 60 slices and 55 dti diffusions i have attached my dmrirc_single_subject file i did the following command: trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject and got the result: INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 INFO: Diffusion root is /Studies/MJMRI/MJ0012 Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Mon Feb 11 12:41:04 CST 2013 mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... Starting DICOMRead2() dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 dcmdir = /Studies/MJMRI/MJ0012//s780 Ref Series No = 13 Found 3304 files, checking for dicoms Found 3300 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 55 nslices = 60 ndcmfiles = 3300 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015
[Freesurfer] warping results on surface
Hi FreeSurfer! A colleague has retinotopic results that he would like to overlay on the FS surface (most likely fsaverage). The retinotopic data is in 2mm isotropic resolution. What would be the best way to be able to overlay this data correctly? Should he first warp the volume to the volume of fsaverage and then use vol2surf? Any help is highly appreciated! Best Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ___ 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] warping results on surface
He should recon-all the anatomical data for the subject, register the fMRI to the anatomical (bbregister), then use mri_vol2surf to map the fMRI to the subject's anatomy. Then use mri_surf2surf to go to fsaverage if needed (though why?). Also, the retinotopy results will look much nicer if the fMRI data are sampled onto the surface and smoothed and analyzed there. doug On 02/12/2013 12:19 PM, Jacobs H (NP) wrote: Hi FreeSurfer! A colleague has retinotopic results that he would like to overlay on the FS surface (most likely fsaverage). The retinotopic data is in 2mm isotropic resolution. What would be the best way to be able to overlay this data correctly? Should he first warp the volume to the volume of fsaverage and then use vol2surf? Any help is highly appreciated! Best Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac...@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Freesurfer version for processed data
Hello, Is there any way to find out which Freesurfer version I used to process data? Thanks, Krista ___ 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] Freesurfer version for processed data
look in the subject/scripts/build-stamp.txt Note that if you set this environment variable setenv REQUIRE_FS_MATCH 1 it will require that a re-running of recon-all use the same version as previous runs doug On 02/12/2013 12:35 PM, krista kelly wrote: Hello, Is there any way to find out which Freesurfer version I used to process data? Thanks, Krista ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Basic skullstrip Inquiry
Hi Gabriel I would run recon-all and see whether the remaining non-brain is included in the surfaces or cerebellum. If not you should be set. I would worry about shaving of gray matter though, which can be difficult to see. cheers Bruce On Tue, 12 Feb 2013, Gabriel Obregon wrote: Hi, I'm using the -gcut flag for the first time and I've noticed that the skull stripping process is still leaving small fragments of dura behind. Will this affect my surfaces? Should I manually edit the brainmask volume to remove as much of these fragments as I can? Also, should I only be concerned about the GM and cerebellum edges when checking for over-aggressive cutting, or are other brain structures important as well, e.g. optic chiasm? Thanks, --G ___ 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] Parallelizing on a different kind of cluster
Thank you very much for your response. Is there a way to use bedpostx instead of bedpostx_seychelles? If not, no worries. I will look at your script and compose one of our own. Best, Susie Kuo On Feb 12, 2013, at 11:56 AM, Anastasia Yendiki wrote: Hi Susie - FSL's bedpostx script works for parallelization on the type of cluster they have at Oxford, and bedpostx_seychelles is a modified version of it that also works on our cluster. Other than that, support for all possible cluster setups at other centers is beyond the scope of our research, but perhaps the existing script is useful as a starting point for making it work on your cluster. Hope this helps, a.y On Tue, 12 Feb 2013, Susan Kuo wrote: Hi TRACULA Experts, Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm on a non-MGH cluster? Thanks! Susie Kuo 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Parallelizing on a different kind of cluster
Everything that's in bedpostx is also in bedpostx_seychelles. I've just added to it. But if you want to run bedpostx directly on the command line instead of going through trac-all -bedp, you can do that, too. On Tue, 12 Feb 2013, Susie Kuo wrote: Thank you very much for your response. Is there a way to use bedpostx instead of bedpostx_seychelles? If not, no worries. I will look at your script and compose one of our own. Best, Susie Kuo On Feb 12, 2013, at 11:56 AM, Anastasia Yendiki wrote: Hi Susie - FSL's bedpostx script works for parallelization on the type of cluster they have at Oxford, and bedpostx_seychelles is a modified version of it that also works on our cluster. Other than that, support for all possible cluster setups at other centers is beyond the scope of our research, but perhaps the existing script is useful as a starting point for making it work on your cluster. Hope this helps, a.y On Tue, 12 Feb 2013, Susan Kuo wrote: Hi TRACULA Experts, Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm on a non-MGH cluster? Thanks! Susie Kuo 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Parallelizing on a different kind of cluster
I see. So I will discriminate between what bedpostx requires from the more inclusive bedpostx_seychelles script. Thank you for your help. I sincerely appreciate it. Best, Susie Kuo On Tue, Feb 12, 2013 at 1:56 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Everything that's in bedpostx is also in bedpostx_seychelles. I've just added to it. But if you want to run bedpostx directly on the command line instead of going through trac-all -bedp, you can do that, too. On Tue, 12 Feb 2013, Susie Kuo wrote: Thank you very much for your response. Is there a way to use bedpostx instead of bedpostx_seychelles? If not, no worries. I will look at your script and compose one of our own. Best, Susie Kuo On Feb 12, 2013, at 11:56 AM, Anastasia Yendiki wrote: Hi Susie - FSL's bedpostx script works for parallelization on the type of cluster they have at Oxford, and bedpostx_seychelles is a modified version of it that also works on our cluster. Other than that, support for all possible cluster setups at other centers is beyond the scope of our research, but perhaps the existing script is useful as a starting point for making it work on your cluster. Hope this helps, a.y On Tue, 12 Feb 2013, Susan Kuo wrote: Hi TRACULA Experts, Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm on a non-MGH cluster? Thanks! Susie Kuo 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/**compliancelinehttp://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 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] preparing NHP data for whole brain analysis
Hi Doug, the issue is that the 112RM atlas is only available as a volume; also, I do not have a surface for one of my subjects. I could either make a surface from the atlas volume and align to that surface for the group analysis, or align the data to the atlas in volume space (if possible) and perform the group analysis in volume space. What would you recommend? Thanks, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu If you can create an average subject and register your individual surfaces to that subject, then it can be done. By default, recon-all will register to the human atlas to create ?h.sphere.reg doug On 02/12/2013 03:57 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thank you very much. One more question: From the documentation, I wasn't really sure whether it would also be possible to do the analysis of the functional data in a common volume space (not MNI, as it is NHP data). Thanks again, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu Hi Caspar, with 5.1 you would not use any of those programs (ie, func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use FSFAST, then see the tutorial for getting started. You'll need to set up the directory structure properly, then run preproc-sess, mkanalysis-sess, and selxavg3-sess. For the group analysis you'll run isxconcat-sess followed by mri_glmfit and mri_glmfit-sim. If you don't have anatomicals for all subjects and you just want to use the average subject, then put the average subject into the subjectname file when you set up the directory structure. doug On 02/12/2013 07:55 AM, Caspar M. Schwiedrzik wrote: Dear Freesurfer experts, I am trying to prepare some NHP functional data for a whole brain group analysis, and I was wondering which sequence of steps you would recommend, given that the data cannot be processed with recon-all. I have surfaces from 4 subjects, but one subject for which I do not have an anatomy of sufficient quality and won't be able to obtain one. I would also like to align the data to the 112RM atlas by Mclaren et al. I was thinking that I could probably align the functional data per subject to the atlas, and then use this registration with func2sph-sess to align all subjects for the group analysis (again to the atlas). Does that make sense, given that I have only four out of five individual surfaces? A second question is when to smooth the data. I assume that it makes most sense to smooth it after it has been transformed into surface space. Would that be sphsmooth-sess? Finally, when doing the analysis, I would use isxavg-re-sess or isxavg-fe-sess, correct? I am using Freesurfer v5.1. Thank you very much for your advice, Caspar __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain
Re: [Freesurfer] preparing NHP data for whole brain analysis
I would recommend using the volume space initially until you can get more surfaces to create your group surface. The one issue with the 112RM_SL is that there is no EPI template. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Feb 12, 2013 at 4:16 PM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi Doug, the issue is that the 112RM atlas is only available as a volume; also, I do not have a surface for one of my subjects. I could either make a surface from the atlas volume and align to that surface for the group analysis, or align the data to the atlas in volume space (if possible) and perform the group analysis in volume space. What would you recommend? Thanks, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu If you can create an average subject and register your individual surfaces to that subject, then it can be done. By default, recon-all will register to the human atlas to create ?h.sphere.reg doug On 02/12/2013 03:57 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thank you very much. One more question: From the documentation, I wasn't really sure whether it would also be possible to do the analysis of the functional data in a common volume space (not MNI, as it is NHP data). Thanks again, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Hi Caspar, with 5.1 you would not use any of those programs (ie, func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use FSFAST, then see the tutorial for getting started. You'll need to set up the directory structure properly, then run preproc-sess, mkanalysis-sess, and selxavg3-sess. For the group analysis you'll run isxconcat-sess followed by mri_glmfit and mri_glmfit-sim. If you don't have anatomicals for all subjects and you just want to use the average subject, then put the average subject into the subjectname file when you set up the directory structure. doug On 02/12/2013 07:55 AM, Caspar M. Schwiedrzik wrote: Dear Freesurfer experts, I am trying to prepare some NHP functional data for a whole brain group analysis, and I was wondering which sequence of steps you would recommend, given that the data cannot be processed with recon-all. I have surfaces from 4 subjects, but one subject for which I do not have an anatomy of sufficient quality and won't be able to obtain one. I would also like to align the data to the 112RM atlas by Mclaren et al. I was thinking that I could probably align the functional data per subject to the atlas, and then use this registration with func2sph-sess to align all subjects for the group analysis (again to the atlas). Does that make sense, given that I have only four out of five individual surfaces? A second question is when to smooth the data. I assume that it makes most sense to smooth it after it has been transformed into surface space. Would that be sphsmooth-sess? Finally, when doing the analysis, I would use isxavg-re-sess or isxavg-fe-sess, correct? I am using Freesurfer v5.1. Thank you very much for your advice, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Re: [Freesurfer] trac-all problem
Hi Jon - Have you run freesurfer (recon-all) on your T1 data? a.y On Tue, 12 Feb 2013, Jon Wieser wrote: i got past the problem with the bvesc, and bvals, my current output has a new problem: here's the last part of the output. #@# Tensor fit Tue Feb 12 15:24:51 CST 2013 dtifit -k /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz -m /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -r /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs -b /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals -o /Studies/MJMRI/MJ0012/freesurfer/dmri/dtifit 0 256 0 256 0 60 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed 44 slices processed 45 slices processed 46 slices processed 47 slices processed 48 slices processed 49 slices processed 50 slices processed 51 slices processed 52 slices processed 53 slices processed 54 slices processed 55 slices processed 56 slices processed 57 slices processed 58 slices processed 59 slices processed #- #@# Priors Tue Feb 12 15:26:36 CST 2013 /Applications/freesurfer/bin/dmri_train --outdir /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni --out lh.cst_AS_avg23_mni_flt rh.cst_AS_avg23_mni_flt lh.ilf_AS_avg23_mni_flt rh.ilf_AS_avg23_mni_flt lh.unc_AS_avg23_mni_flt rh.unc_AS_avg23_mni_flt fmajor_PP_avg23_mni_flt fminor_PP_avg23_mni_flt lh.atr_PP_avg23_mni_flt rh.atr_PP_avg23_mni_flt lh.cab_PP_avg23_mni_flt rh.cab_PP_avg23_mni_flt lh.ccg_PP_avg23_mni_flt rh.ccg_PP_avg23_mni_flt lh.slfp_PP_avg23_mni_flt rh.slfp_PP_avg23_mni_flt lh.slft_PP_avg23_mni_flt rh.slft_PP_avg23_mni_flt --slist /tmp/subj23.freesurfer.92196.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2! .flt.nii .gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lowb_brain_mask.flt.nii.gz --fa /Studies/MJMRI/MJ0012/freesurfer/dmri/mni/dtifit_FA.flt.nii.gz --ncpts 5 --debug ERROR: fio_pushd: /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni ERROR: must specify brain mask volume for output subject Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Feb 12 15:26:36 CST 2013 what is the brainmask volume that
Re: [Freesurfer] trac-all problem
and yes, you'll need to run recon-all on your data before running tracula cheers Bruce On Tue, 12 Feb 2013, Anastasia Yendiki wrote: Hi Jon - You'll the aparc+aseg.mgz (cortical parcellation + subcortical segmentation). The basis of TRACULA is that it uses the underlying anatomy to reconstruct the tracts. a.y On Tue, 12 Feb 2013, Jon Wieser wrote: no i have not run recon-all yet on this dataset, do i need to run recon-all with -autorecon1 ,-autorecon2, and -autorecon3 before i analyze the dti data? thanks Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, February 12, 2013 3:34:19 PM Subject: Re: [Freesurfer] trac-all problem Hi Jon - Have you run freesurfer (recon-all) on your T1 data? a.y On Tue, 12 Feb 2013, Jon Wieser wrote: i got past the problem with the bvesc, and bvals, my current output has a new problem: here's the last part of the output. #@# Tensor fit Tue Feb 12 15:24:51 CST 2013 dtifit -k /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz -m /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -r /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs -b /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals -o /Studies/MJMRI/MJ0012/freesurfer/dmri/dtifit 0 256 0 256 0 60 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed 44 slices processed 45 slices processed 46 slices processed 47 slices processed 48 slices processed 49 slices processed 50 slices processed 51 slices processed 52 slices processed 53 slices processed 54 slices processed 55 slices processed 56 slices processed 57 slices processed 58 slices processed 59 slices processed #- #@# Priors Tue Feb 12 15:26:36 CST 2013 /Applications/freesurfer/bin/dmri_train --outdir /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni --out lh.cst_AS_avg23_mni_flt rh.cst_AS_avg23_mni_flt lh.ilf_AS_avg23_mni_flt rh.ilf_AS_avg23_mni_flt lh.unc_AS_avg23_mni_flt rh.unc_AS_avg23_mni_flt fmajor_PP_avg23_mni_flt fminor_PP_avg23_mni_flt lh.atr_PP_avg23_mni_flt rh.atr_PP_avg23_mni_flt lh.cab_PP_avg23_mni_flt rh.cab_PP_avg23_mni_flt lh.ccg_PP_avg23_mni_flt rh.ccg_PP_avg23_mni_flt lh.slfp_PP_avg23_mni_flt rh.slfp_PP_avg23_mni_flt lh.slft_PP_avg23_mni_flt rh.slft_PP_avg23_mni_flt --slist /tmp/subj23.freesurfer.92196.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dl abel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2! .flt.nii .gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz
[Freesurfer] R: Re: R: trac-all -path error
Hi Anastasia, thanks! I hope that is all ok in Boston. I'm attaching the configuration file that I'm using. I'd like ask you if/how I can also run the second step of trac-all (bedpostx) using FSL on other pc? May I directly run in FSL dmri folder? Do you think that I should rename some files? An additional question. For some subjects (no for subject that I'm running with the config file that I have attached) I have 16 direction and b=0 is the last of these. Is the nb0=16? Thank you very much. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 12-feb-2013 17.45 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: trac-all -path error Hi Stefano - There is no need to attach the trac-all script, I am quite familiar with it. Perhaps you could attach the configuration file that you set up? Thanks, a.y On Mon, 11 Feb 2013, std...@virgilio.it wrote: I'm attaching my trac-all file for check.Thanks, Stefano Messaggio originale Da: std...@virgilio.it Data: 11-feb-2013 14.42 A: freesurfer@nmr.mgh.harvard.edu Cc: ayend...@nmr.mgh.harvard.edu Ogg: [Freesurfer] trac-all -path error Hi list, I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I have this error: Loading mask from /Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX niiRead(): error opening file /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz From http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22066.html I'm deducing that the error may be related trace-all upload. I have doing this upload but I visualize always the same error. I attached tract-all uploades file that live in /Applications/freesurfer/bin. Please, could you check it? I have also other question. May I run the second step of trac-all (bedpostx) using FSL on other pc? In this way, could I directly run in FSL dmri folder? Do you think that I should rename some files? Thanks, Stefano ___ 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. dmrirc_single_subject_d1 Description: Binary data ___ 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] R: Re: R: trac-all -path error
Hi Stefano - All is well here, thank you. Yes, you can run bedpostx directly on the dmri directory. If you search for bedpostx in the freesurfer email list archives, you'll find the info you need since other people have done this before. a.y On Tue, 12 Feb 2013, std...@virgilio.it wrote: Hi Anastasia, thanks! I hope that is all ok in Boston. I'm attaching the configuration file that I'm using. I'd like ask you if/how I can also run the second step of trac-all (bedpostx) using FSL on other pc? May I directly run in FSL dmri folder? Do you think that I should rename some files? An additional question. For some subjects (no for subject that I'm running with the config file that I have attached) I have 16 direction and b=0 is the last of these. Is the nb0=16? Thank you very much. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 12-feb-2013 17.45 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: trac-all -path error Hi Stefano - There is no need to attach the trac-all script, I am quite familiar with it. Perhaps you could attach the configuration file that you set up? Thanks, a.y On Mon, 11 Feb 2013, std...@virgilio.it wrote: I'm attaching my trac-all file for check.Thanks, Stefano Messaggio originale Da: std...@virgilio.it Data: 11-feb-2013 14.42 A: freesurfer@nmr.mgh.harvard.edu Cc: ayend...@nmr.mgh.harvard.edu Ogg: [Freesurfer] trac-all -path error Hi list, I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I have this error: Loading mask from /Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX niiRead(): error opening file /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz From http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22066.html I'm deducing that the error may be related trace-all upload. I have doing this upload but I visualize always the same error. I attached tract-all uploades file that live in /Applications/freesurfer/bin. Please, could you check it? I have also other question. May I run the second step of trac-all (bedpostx) using FSL on other pc? In this way, could I directly run in FSL dmri folder? Do you think that I should rename some files? Thanks, Stefano ___ 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 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] R: R: Re: R: trac-all -path error
Thank you Anastasia. But I do not understand why I have the error in trac-all -path. The configuration file that I have attached is good? Stefano Messaggio originale Da: std...@virgilio.it Data: 12-feb-2013 23.27 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: R: trac-all -path error Hi Anastasia, thanks! I hope that is all ok in Boston. I'm attaching the configuration file that I'm using. I'd like ask you if/how I can also run the second step of trac-all (bedpostx) using FSL on other pc? May I directly run in FSL dmri folder? Do you think that I should rename some files? An additional question. For some subjects (no for subject that I'm running with the config file that I have attached) I have 16 direction and b=0 is the last of these. Is the nb0=16? Thank you very much. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 12-feb-2013 17.45 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: trac-all -path error Hi Stefano - There is no need to attach the trac-all script, I am quite familiar with it. Perhaps you could attach the configuration file that you set up? Thanks, a.y On Mon, 11 Feb 2013, std...@virgilio.it wrote: I'm attaching my trac-all file for check.Thanks, Stefano Messaggio originale Da: std...@virgilio.it Data: 11-feb-2013 14.42 A: freesurfer@nmr.mgh.harvard.edu Cc: ayend...@nmr.mgh.harvard.edu Ogg: [Freesurfer] trac-all -path error Hi list, I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I have this error: Loading mask from /Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX niiRead(): error opening file /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz From http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22066.html I'm deducing that the error may be related trace-all upload. I have doing this upload but I visualize always the same error. I attached tract-all uploades file that live in /Applications/freesurfer/bin. Please, could you check it? I have also other question. May I run the second step of trac-all (bedpostx) using FSL on other pc? In this way, could I directly run in FSL dmri folder? Do you think that I should rename some files? Thanks, Stefano ___ 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 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] R: R: Re: R: trac-all -path error
Hi Stefano - The order of the 3 trac-all steps is not inter-changeable. You need to run bedpostx *before* you can run the path reconstruction. a.y On Wed, 13 Feb 2013, std...@virgilio.it wrote: Thank you Anastasia. But I do not understand why I have the error in trac-all -path. The configuration file that I have attached is good? Stefano Messaggio originale Da: std...@virgilio.it Data: 12-feb-2013 23.27 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: R: trac-all -path error Hi Anastasia, thanks! I hope that is all ok in Boston. I'm attaching the configuration file that I'm using. I'd like ask you if/how I can also run the second step of trac-all (bedpostx) using FSL on other pc? May I directly run in FSL dmri folder? Do you think that I should rename some files? An additional question. For some subjects (no for subject that I'm running with the config file that I have attached) I have 16 direction and b=0 is the last of these. Is the nb0=16? Thank you very much. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 12-feb-2013 17.45 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: trac-all -path error Hi Stefano - There is no need to attach the trac-all script, I am quite familiar with it. Perhaps you could attach the configuration file that you set up? Thanks, a.y On Mon, 11 Feb 2013, std...@virgilio.it wrote: I'm attaching my trac-all file for check.Thanks, Stefano Messaggio originale Da: std...@virgilio.it Data: 11-feb-2013 14.42 A: freesurfer@nmr.mgh.harvard.edu Cc: ayend...@nmr.mgh.harvard.edu Ogg: [Freesurfer] trac-all -path error Hi list, I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I have this error: Loading mask from /Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX niiRead(): error opening file /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz From http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22066.html I'm deducing that the error may be related trace-all upload. I have doing this upload but I visualize always the same error. I attached tract-all uploades file that live in /Applications/freesurfer/bin. Please, could you check it? I have also other question. May I run the second step of trac-all (bedpostx) using FSL on other pc? In this way, could I directly run in FSL dmri folder? Do you think that I should rename some files? Thanks, Stefano ___ 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 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] matrix design to homogeneity of slopes designs
The matrix that you have will fail because Col1+Col2=Col3 (and same for the other columns). To do what you want, use the DODS that mri_glmfit generates along with a contrast of [0 0 1 -1]. The constant term is modelled by the first two columns. doug On 02/12/2013 03:19 PM, jm wrote: Hi fs experts, I need to execute *mri_glmfit* with -X option to probe interactions between Diagnosis and Age, Statistic Software help suggest: The*homogeneity of slopes designs* can be used to test whether the continuous and categorical predictors interact in influencing responses, and thus, whether the traditional ANCOVA design or the separate slope file:///textbook/general-linear-models/#between_subject design is appropriate for modeling the effects of the predictor. for 2 groups thickness = b_0 + b_1 X_1 + b_2 X_2 + b_3 * Age + b4 X1*Age + b5 x2*Age the Matrix Design Xm _corresponding 1 1 0 56 56 0 1 1 0 67 67 0 1 1 0 67 67 0 1 1 0 78 78 0 1 1 0 67 67 0 1 1 0 87 87 0 1 0 1 67 0 67 1 0 1 66 0 66 1 0 1 65 0 65 1 0 1 87 0 87 1 0 1 45 0 45 1 0 1 77 0 77 In matrix design generated by freesurfer _*file Xg.dat*_ for both DODS and DOSS the first column don't appears. Constant term is not explicitly considered my question is: is correct to use *mri_glmfit* with -X Xm as above specified ? or I need to eliminate the first column? 1 0 56 56 0 1 0 67 67 0 1 0 67 67 0 1 0 78 78 0 1 0 67 67 0 1 0 87 87 0 0 1 67 0 67 0 1 66 0 66 0 1 65 0 65 0 1 87 0 87 0 1 45 0 45 0 1 77 0 77 thanks!! ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] LME - contrast
Dear Jorge, For the statistical analysis of longitudinal data we used the Two Stage Model (TSM) and the Linear Mixed Effects. Our intergroup LME results (2 groups, 2 time points) had many similarities with TSM results. Then with TSM we analysed the intragroup changes (one group, and 2 time points). We tried to do the same analysis with LME but the results are very different, so I suppose that the contrast was incorrect. For the intergroup analysis (2 groups x 2 time points) I used /lme_mass_fit_vw/ and CM.C = [0 0 0 1]; For the intragroup (1 group x 2 time points) I also used /lme_mass_fit_vw/ but CM.C = [0 1]; Can you please tell me if the CM.C is correct ? or is there something else I should change ? Thanks, Best regards, Alex. ___ 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] preparing NHP data for whole brain analysis
Thanks for your input, Donald. Unfortunately, I won't be able to acquire the missing high quality anatomy. Doug, I did not get from the documentation how to use preproc-sess to align data to an NHP atlas in volume space (that is not in human MNI space). Please advise. Thanks! Caspar 2013/2/12 MCLAREN, Donald mclaren.don...@gmail.com I would recommend using the volume space initially until you can get more surfaces to create your group surface. The one issue with the 112RM_SL is that there is no EPI template. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Feb 12, 2013 at 4:16 PM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi Doug, the issue is that the 112RM atlas is only available as a volume; also, I do not have a surface for one of my subjects. I could either make a surface from the atlas volume and align to that surface for the group analysis, or align the data to the atlas in volume space (if possible) and perform the group analysis in volume space. What would you recommend? Thanks, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu If you can create an average subject and register your individual surfaces to that subject, then it can be done. By default, recon-all will register to the human atlas to create ?h.sphere.reg doug On 02/12/2013 03:57 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thank you very much. One more question: From the documentation, I wasn't really sure whether it would also be possible to do the analysis of the functional data in a common volume space (not MNI, as it is NHP data). Thanks again, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Hi Caspar, with 5.1 you would not use any of those programs (ie, func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use FSFAST, then see the tutorial for getting started. You'll need to set up the directory structure properly, then run preproc-sess, mkanalysis-sess, and selxavg3-sess. For the group analysis you'll run isxconcat-sess followed by mri_glmfit and mri_glmfit-sim. If you don't have anatomicals for all subjects and you just want to use the average subject, then put the average subject into the subjectname file when you set up the directory structure. doug On 02/12/2013 07:55 AM, Caspar M. Schwiedrzik wrote: Dear Freesurfer experts, I am trying to prepare some NHP functional data for a whole brain group analysis, and I was wondering which sequence of steps you would recommend, given that the data cannot be processed with recon-all. I have surfaces from 4 subjects, but one subject for which I do not have an anatomy of sufficient quality and won't be able to obtain one. I would also like to align the data to the 112RM atlas by Mclaren et al. I was thinking that I could probably align the functional data per subject to the atlas, and then use this registration with func2sph-sess to align all subjects for the group analysis (again to the atlas). Does that make sense, given that I have only four out of five individual surfaces? A second question is when to smooth the data. I assume that it makes most sense to smooth it after it has been transformed into surface space. Would that be sphsmooth-sess? Finally, when doing the analysis, I would use isxavg-re-sess or isxavg-fe-sess, correct? I am using Freesurfer v5.1. Thank you very much for your advice, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] preparing NHP data for whole brain analysis
If you can get good alignment between the EPI and the T1 images for the 4 subjects with good T1 images, you might try the following: (1) coregister each T1 to the corresponding EPI; (2) normalize the coregistered T1 to the 112RM-SL atlas (see McLaren et al. 2010 in Methods for your options) (3) apply the normalization to EPI data (4) create a mean image from the 4 monkeys (call this the 112RM-SL_EPI and make it public after you publish your paper). (5) use the new EPI atlas to normalize the EPI images. This way all 5 monkeys are aligned to the same template space. If you can create the EPI template in a separate set of animals not in the current experiment, it would be better. You might want to contact Justin Vincent to see if he know any good EPI and T1 datasets in monkeys that could be used to make an EPI template or surfaces for a 112RM-SL surface atlas. Hope this helps. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Feb 12, 2013 at 6:44 PM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Thanks for your input, Donald. Unfortunately, I won't be able to acquire the missing high quality anatomy. Doug, I did not get from the documentation how to use preproc-sess to align data to an NHP atlas in volume space (that is not in human MNI space). Please advise. Thanks! Caspar 2013/2/12 MCLAREN, Donald mclaren.don...@gmail.com I would recommend using the volume space initially until you can get more surfaces to create your group surface. The one issue with the 112RM_SL is that there is no EPI template. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Feb 12, 2013 at 4:16 PM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi Doug, the issue is that the 112RM atlas is only available as a volume; also, I do not have a surface for one of my subjects. I could either make a surface from the atlas volume and align to that surface for the group analysis, or align the data to the atlas in volume space (if possible) and perform the group analysis in volume space. What would you recommend? Thanks, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu If you can create an average subject and register your individual surfaces to that subject, then it can be done. By default, recon-all will register to the human atlas to create ?h.sphere.reg doug On 02/12/2013 03:57 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thank you very much. One more question: From the documentation, I wasn't really sure whether it would also be possible to do the analysis of the functional data in a common volume space (not MNI, as it is NHP data). Thanks again, Caspar 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Hi Caspar, with 5.1 you would not use any of those programs (ie, func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use FSFAST, then see the tutorial
Re: [Freesurfer] LME - contrast
Hi Alex Certainly, for such a simple design matrix, only two repeated measures per subject with a small inter-subject variability in between-scan time interval and a very small number of subjects with a single time point the results from both procedures should not be very different. Furthermore, by using TSM you have the additional possibility of applying cluster-wise simulation-based multiple comparison procedures implemented in Freesurfer. LME must be used to address more complicated designs with time-varying covariates, variable timing across subjects, variable drop-out rate across measurement occasions, different number of repeated measures across subjects (even a single time point) and subjects with more than three repeated measures. For your intra-group analyses using LME you simply need to test whether group-specific slopes of change are different from zero. You don't need to fit the model again for this. For the reference group you should simply test the coefficient of the time variable: CM.C = [0 1 0 0] and for the other group the contrast is given by the sum of the previous coefficient and the coefficient of the interaction term: CM.C = [0 1 0 1] Best -Jorge De: Alex Hanganu al.hang...@yahoo.ca Para: FS Mailing List Freesurfer@nmr.mgh.harvard.edu; Jorge L. Bernal-Rusiel jber...@nmr.mgh.harvard.edu Enviado: Martes 12 de febrero de 2013 18:29 Asunto: [Freesurfer] LME - contrast Dear Jorge, For the statistical analysis of longitudinal data we used the Two Stage Model (TSM) and the Linear Mixed Effects. Our intergroup LME results (2 groups, 2 time points) had many similarities with TSM results. Then with TSM we analysed the intragroup changes (one group, and 2 time points). We tried to do the same analysis with LME but the results are very different, so I suppose that the contrast was incorrect. For the intergroup analysis (2 groups x 2 time points) I used lme_mass_fit_vw and CM.C = [0 0 0 1]; For the intragroup (1 group x 2 time points) I also used lme_mass_fit_vw but CM.C = [0 1]; Can you please tell me if the CM.C is correct ? or is there something else I should change ? Thanks, Best regards, Alex. ___ 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 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.
