Re: [Freesurfer] TRACULA bvecs question
Dear Priti, Anastasia, Thank you for your help, I created bvec and bval files and it went fine. But now I have another error in preprocessing step. I attach a log file. Could you please take a look at that? Thank you, Tanja. trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012 On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs was created at all? It looks like that may not have been created and that's why it can't find dwi_orig_flip.mghdti.bvecs. If your bvals and bvecs information is not encoded in the dicom header, then you can specify it explicitly in the dmrirc file. Please refer to the following page for instructions on how to specify your bvals and bvecs for tracula: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Hope this helps, Priti Hi Priti, I changed the dmrirc file to the one you sent, but unfortunately got the same error. I attach the log (although it is basically the same). Do you have any ideas what else can cause it? Thanks again, Tanja. On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, I think the problem may be due to the trailing slash you've included while specifying $dtroot, $SUBJECTS_DIR etc. setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/ should be setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1 trac-all usually adds the '/' and since you're adding an extra '/', it's giving an error. I've edited your dmrirc file and removed those trailing slashes. Could you run this again and let us know if it solves the problem? Hope this is helpful, Priti Thank you Priti and Anastasia, Anastasia, just wanted to clarify, I meant $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for this misunderstanding. I attach my configuration file and the command I use is trac-all -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc . I also attach a picture of my file tree and a track-all.log file. Thank you for your time and help, Tanja. On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Tanja - The file is supposed to be created under $dtroot/$subjectname/dmri/bvecs. If it's trying to create it as /dmri/bvecs, this means that something wasn't defined correctly. What is the exact trac-all command line that you're using? And your configuration file if you're using one? a.y On Thu, 2 Feb 2012, Tetiana Dadakova wrote: Dear list, I try to run TRACULA pre-processing step and I get the following error: /dmri/bvecs: No such file or directory. I have a folder with reconstructed T1 data and a folder with raw dicom DTI data. When I start trac-all -prep, it creates directory /dmri/, but it doesn't create the bvecs file. Should I create it myself using dcm2nii or is it supposed to be created automatically? Thank you, Tanja. ___ 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. trac-all.log 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] Comparing Cortical Thickness
Hi Jeff, I think you want to use Doug's tools for this (mri_glm and such). He'll probably comment in an hour or two cheers Bruce On Mon, 13 Feb 2012, Jeff Sadino wrote: Hello FreeSurfers, I want to compare cortical thickness differences between my two groups. Is this the correct pipeline? I ran make_average_subject on each group. To get the study thickness file in control space, I did this: mri_surf2surf --srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control --trgsurfval control/surf/study.thickness.mgh --hemi lh And then to calculate the differences, I used: mris_thickness_diff -out diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial control/surf/study.thickness.mgh. Is this the right way to do this? mris_thickness_diff says it should only be used on the same subject. mris_diff says it is still being tested. I also see mris_thickness_comparison. Which command is the best to use to get a thickness difference map? Thank you very much, Jeff Sadino ___ 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] Comparing Cortical Thickness
Hi Jeff, you should use mris_preproc to stack the subjects into one file, mri_surf2surf to smooth them, and mri_glmfit to analyze them (including computing the difference between groups and other stats). See the group tutorial on the web page. You could probably do what you are suggesting, but it takes you off the usual pipeline and would be a dead end in the case that you wanted to take the next step such as computing p-values. doug On 2/14/12 9:15 AM, Bruce Fischl wrote: Hi Jeff, I think you want to use Doug's tools for this (mri_glm and such). He'll probably comment in an hour or two cheers Bruce On Mon, 13 Feb 2012, Jeff Sadino wrote: Hello FreeSurfers, I want to compare cortical thickness differences between my two groups. Is this the correct pipeline? I ran make_average_subject on each group. To get the study thickness file in control space, I did this: mri_surf2surf --srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control --trgsurfval control/surf/study.thickness.mgh --hemi lh And then to calculate the differences, I used: mris_thickness_diff -out diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial control/surf/study.thickness.mgh. Is this the right way to do this? mris_thickness_diff says it should only be used on the same subject. mris_diff says it is still being tested. I also see mris_thickness_comparison. Which command is the best to use to get a thickness difference map? Thank you very much, Jeff Sadino ___ 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] Comparing Cortical Thickness
Hi Jeff, make_average_subject is just if you want to visualize results on a surface presenting the average of your own subjects, rather than using the provided 'fsaverage'. It is not necessary (and not related) to performing group statistical comparisons per se. You can use the 'qdec' utility to do compute maps of groupwise statisical differences on the surface, after first running recon-all with the -qcache flag. cheers, -MH On Mon, 2012-02-13 at 20:06 -1000, Jeff Sadino wrote: Hello FreeSurfers, I want to compare cortical thickness differences between my two groups. Is this the correct pipeline? I ran make_average_subject on each group. To get the study thickness file in control space, I did this: mri_surf2surf --srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control --trgsurfval control/surf/study.thickness.mgh -- hemi lh And then to calculate the differences, I used: mris_thickness_diff - out diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial control/surf/study.thickness.mgh. Is this the right way to do this? mris_thickness_diff says it should only be used on the same subject. mris_diff says it is still being tested. I also see mris_thickness_comparison. Which command is the best to use to get a thickness difference map? Thank you very much, Jeff Sadino ___ 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
Re: [Freesurfer] Clusters locations
Hi Antonella, what level of detail do you want? I think that most people are reporting MNI coordinates. doug On 2/13/12 2:44 PM, Antonella Kis wrote: Hi Doug, I will be very grateful if you give me some directions regarding how I can get my clusters location ( my output is too general telling me just Left-Cerebral-White-Matter and Right-Cerebral-White-Matter) and the coordinates (MNI) when I run the: mri_volcluster --in GroupAnalysis_pos.glmdir/contrast/sig.mgh --mask GroupAnalysis_pos.glmdir/mask.mgh --no-fixmni --cwsig GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .09 --seg cvs_avg35 aseg.mgz --csdpdf GroupAnalysis_pos.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_pos.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_pos.glmdir/contrast/permcsd.sig.voxel.mgh and mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis-FA-MASKED.ANAT+CVS-to-avg35.nii.gz --avgwf fa.avg.dat --sum permcsd.sig.cluster.summary Thank you. Antonella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_volcluster register.dat question
Hello all, I'm trying to run mri_volcluster on our third-level functional data and one of the required flagged arguments is the register.dat file. Our data preprocessing/registration was done in FSL, not Freesurfer, so we don't have this particular file. Is there anything we can do to get around this or do we need to run tkregister first in order to use mri_volcluster? Thanks for your time. -Huiting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_vol2surf
Dear FreeSurfers, To get a better view on the pial surface of the Heschl' Gyri I used the command mri_vol2surf after having created the suitable label with (label2vol). My goal is to get My Command was: *mri_vol2surf --src pf_lh_vol.mgz --hemi lh --srcreg register.dat --out_type paint --o A1surf-lh.w* The output file was created without any error, but loading the file in freeview or tksurfer an error occured: *command: tksurfer WH lh A1surf-lh.w* * * *subject is WH* *hemiis lh* *surface is A1surf-lh.w* *surfer: current subjects dir: /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide* *surfer: not in scripts dir == using cwd for session root* *surfer: session root data dir ($session) set to:* *surfer: /freesurfer/Kontrollen/A1_Wilts_Heide* *checking for nofix files in 'A1surf-lh.w'* *Reading image info (/Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH)* *Reading /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/mri/orig.mgz* *surfer: Reading header info from /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/mri/orig.mgz* *ERROR: MRISread: file '/Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/surf/lh.A1surf-lh.w' has 0 vertices!* *Probably trying to use a scalar data file as a surface!* * * Any help would be greatly appreciated. Thanks in advance Holger ___ 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] TRACULA bvecs question
You need to set the nb0 parameter (number of low-b volumes in the beginning of your DWI series). On Tue, 14 Feb 2012, Tetiana Dadakova wrote: Dear Priti, Anastasia, Thank you for your help, I created bvec and bval files and it went fine. But now I have another error in preprocessing step. I attach a log file. Could you please take a look at that? Thank you, Tanja. trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012 On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs was created at all? It looks like that may not have been created and that's why it can't find dwi_orig_flip.mghdti.bvecs. If your bvals and bvecs information is not encoded in the dicom header, then you can specify it explicitly in the dmrirc file. Please refer to the following page for instructions on how to specify your bvals and bvecs for tracula: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Hope this helps, Priti Hi Priti, I changed the dmrirc file to the one you sent, but unfortunately got the same error. I attach the log (although it is basically the same). Do you have any ideas what else can cause it? Thanks again, Tanja. On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, I think the problem may be due to the trailing slash you've included while specifying $dtroot, $SUBJECTS_DIR etc. setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/ should be setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1 trac-all usually adds the '/' and since you're adding an extra '/', it's giving an error. I've edited your dmrirc file and removed those trailing slashes. Could you run this again and let us know if it solves the problem? Hope this is helpful, Priti Thank you Priti and Anastasia, Anastasia, just wanted to clarify, I meant $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for this misunderstanding. I attach my configuration file and the command I use is trac-all -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc . I also attach a picture of my file tree and a track-all.log file. Thank you for your time and help, Tanja. On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Tanja - The file is supposed to be created under $dtroot/$subjectname/dmri/bvecs. If it's trying to create it as /dmri/bvecs, this means that something wasn't defined correctly. What is the exact trac-all command line that you're using? And your configuration file if you're using one? a.y On Thu, 2 Feb 2012, Tetiana Dadakova wrote: Dear list, I try to run TRACULA pre-processing step and I get the following error: /dmri/bvecs: No such file or directory. I have a folder with reconstructed T1 data and a folder with raw dicom DTI data. When I start trac-all -prep, it creates directory /dmri/, but it doesn't create the bvecs file. Should I create it myself using dcm2nii or is it supposed to be created automatically? Thank you, Tanja. ___ 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
Re: [Freesurfer] TRACULA bvecs question
PS: The info on what you need to set it here: https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc # Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 10 On Tue, 14 Feb 2012, Tetiana Dadakova wrote: Dear Priti, Anastasia, Thank you for your help, I created bvec and bval files and it went fine. But now I have another error in preprocessing step. I attach a log file. Could you please take a look at that? Thank you, Tanja. trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012 On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs was created at all? It looks like that may not have been created and that's why it can't find dwi_orig_flip.mghdti.bvecs. If your bvals and bvecs information is not encoded in the dicom header, then you can specify it explicitly in the dmrirc file. Please refer to the following page for instructions on how to specify your bvals and bvecs for tracula: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Hope this helps, Priti Hi Priti, I changed the dmrirc file to the one you sent, but unfortunately got the same error. I attach the log (although it is basically the same). Do you have any ideas what else can cause it? Thanks again, Tanja. On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, I think the problem may be due to the trailing slash you've included while specifying $dtroot, $SUBJECTS_DIR etc. setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/ should be setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1 trac-all usually adds the '/' and since you're adding an extra '/', it's giving an error. I've edited your dmrirc file and removed those trailing slashes. Could you run this again and let us know if it solves the problem? Hope this is helpful, Priti Thank you Priti and Anastasia, Anastasia, just wanted to clarify, I meant $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for this misunderstanding. I attach my configuration file and the command I use is trac-all -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc . I also attach a picture of my file tree and a track-all.log file. Thank you for your time and help, Tanja. On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Tanja - The file is supposed to be created under $dtroot/$subjectname/dmri/bvecs. If it's trying to create it as /dmri/bvecs, this means that something wasn't defined correctly. What is the exact trac-all command line that you're using? And your configuration file if you're using one? a.y On Thu, 2 Feb 2012, Tetiana Dadakova wrote: Dear list, I try to run TRACULA pre-processing step and I get the following error: /dmri/bvecs: No such file or directory. I have a folder with reconstructed T1 data and a folder with raw dicom DTI data. When I start trac-all -prep, it creates directory /dmri/, but it doesn't create the bvecs file. Should I create it myself using dcm2nii or is it supposed to be created automatically? Thank you, Tanja. ___ 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
Re: [Freesurfer] mri_volcluster register.dat question
Hi Huiting, you don't need to give it a register.dat. That only gives you access to label locations of your clusters. If this is something you want, you can use $FREESURFER_HOME/average/mni152.register.dat. doug Huiting Liu wrote: Hello all, I'm trying to run mri_volcluster on our third-level functional data and one of the required flagged arguments is the register.dat file. Our data preprocessing/registration was done in FSL, not Freesurfer, so we don't have this particular file. Is there anything we can do to get around this or do we need to run tkregister first in order to use mri_volcluster? Thanks for your time. -Huiting ___ 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 ___ 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] Clusters locations
Antonella Kis wrote: Hi Doug, 1) I would like to report the MNI coordinates and also a more exactly region I mean if possible tto find exactly where in the Left-Cerebral-White-Matter and Right-Cerebral-White-Matter my cluster is located. What do you me by exactly where? The nearest cortical label? The fiber bundle? 2)Can you please tell me if for the mean diffusivity I should use the simulation with the perm (as I use for the FA due to the fact that is not so Gaussian) option or it is OK to use the grf option. I think you can use GRF for this as it corresponds to a normal contrast in a GLM. Note that the permutation is the stronger (but more conservative) test. 3) Can you please explain what exactly means for my clusters if I hit the positive sign under DISPLAY in Qdec? I mean if I compare the cortical thickness between two classes: controls vs. Patients and I am not interested in the sex or age differences just differences between the two classes will positive mean clusters where cortical thickness graeter in Class 1 than Class2 (Class1Class2)? I have C = +1 -1 and my Class 1 = controls while Class2 = PAtients. Positive is Controls Patients doug THANKS YOU. Antonella *From:* Douglas Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com; free surfer freesurfer@nmr.mgh.harvard.edu *Sent:* Tuesday, February 14, 2012 9:59 AM *Subject:* Re: [Freesurfer] Clusters locations Hi Antonella, what level of detail do you want? I think that most people are reporting MNI coordinates. doug On 2/13/12 2:44 PM, Antonella Kis wrote: Hi Doug, I will be very grateful if you give me some directions regarding how I can get my clusters location ( my output is too general telling me just Left-Cerebral-White-Matter and Right-Cerebral-White-Matter) and the coordinates (MNI) when I run the: mri_volcluster --in GroupAnalysis_pos.glmdir/contrast/sig.mgh --mask GroupAnalysis_pos.glmdir/mask.mgh --no-fixmni --cwsig GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .09 --seg cvs_avg35 aseg.mgz --csdpdf GroupAnalysis_pos.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_pos.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_pos.glmdir/contrast/permcsd.sig.voxel.mgh and mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis-FA-MASKED.ANAT+CVS-to-avg35.nii.gz --avgwf fa.avg.dat --sum permcsd.sig.cluster.summary Thank you. Antonella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. -- 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] (no subject)
Hi, I am trying to use selxavg3-sess function and getting this error. Below is the error I get. I actually have this fingertap.par file but freesurfer somehow does not see it. Any help would be appreciated. Thanks! Meryem Yucel PMI Lab Extension format = nii.gz ERROR: opening /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/fingertap No such file or directory ??? Output argument partype (and maybe others) not assigned during call to /usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_ldpar4.m (fast_ldpar4). Error in == fast_ldpar4 at 45 par4 = []; Error in == flac_customize at 121 [par partype] = fast_ldpar4(parpath); Error in == fast_selxavg3 at 65 flac0 = flac_customize(flac0); ___ 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] Extraction of vertex identifiers from a significant cluster
Dear all, We have performed a cluster analysis in Qdec and found a significant vertex-cluster after correction for multiple testing using the Monte Carlo simulation. Now, we would like to extract the (unique) identifiers of all vertices that form the significant cluster. We then would like to look up the spatial information (x, y, z) of these vertices. Our final aim is to map the vertices to an atlas which is different from that of Desikan. Is this a way suitable to achieve our aim? Many thanks for your help in advance! Best regards, Florian -- Florian Siedek Doctoral Scientist Institute of Human Genetics Department of Genomics Life Brain Center University of Bonn Sigmund-Freud-Strasse 25 D-53127 Bonn Germany Email: flor...@gmail.com ___ 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] TRACULA bvecs question
I see, thank you :) On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: PS: The info on what you need to set it here: https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc # Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 10 On Tue, 14 Feb 2012, Tetiana Dadakova wrote: Dear Priti, Anastasia, Thank you for your help, I created bvec and bval files and it went fine. But now I have another error in preprocessing step. I attach a log file. Could you please take a look at that? Thank you, Tanja. trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012 On Fri, Feb 3, 2012 at 5:52 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs was created at all? It looks like that may not have been created and that's why it can't find dwi_orig_flip.mghdti.bvecs. If your bvals and bvecs information is not encoded in the dicom header, then you can specify it explicitly in the dmrirc file. Please refer to the following page for instructions on how to specify your bvals and bvecs for tracula: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Hope this helps, Priti Hi Priti, I changed the dmrirc file to the one you sent, but unfortunately got the same error. I attach the log (although it is basically the same). Do you have any ideas what else can cause it? Thanks again, Tanja. On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan rspr...@nmr.mgh.harvard.edu wrote: Hi Tanja, I think the problem may be due to the trailing slash you've included while specifying $dtroot, $SUBJECTS_DIR etc. setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/ should be setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1 trac-all usually adds the '/' and since you're adding an extra '/', it's giving an error. I've edited your dmrirc file and removed those trailing slashes. Could you run this again and let us know if it solves the problem? Hope this is helpful, Priti Thank you Priti and Anastasia, Anastasia, just wanted to clarify, I meant $dtroot/$subjectname/dmri/bvecs, when I wrote /dmri/bvecs, sorry for this misunderstanding. I attach my configuration file and the command I use is trac-all -prep -c /Applications/freesurfer/subjects/TRACULA/DTI/scripts/dmrirc . I also attach a picture of my file tree and a track-all.log file. Thank you for your time and help, Tanja. On Fri, Feb 3, 2012 at 2:21 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Tanja - The file is supposed to be created under $dtroot/$subjectname/dmri/bvecs. If it's trying to create it as /dmri/bvecs, this means that something wasn't defined correctly. What is the exact trac-all command line that you're using? And your configuration file if you're using one? a.y On Thu, 2 Feb 2012, Tetiana Dadakova wrote: Dear list, I try to run TRACULA pre-processing step and I get the following error: /dmri/bvecs: No such file or directory. I have a folder with reconstructed T1 data and a folder with raw dicom DTI data. When I start trac-all -prep, it creates directory /dmri/, but it doesn't create the bvecs file. Should I create it myself using dcm2nii or is it supposed to be created automatically? Thank you, Tanja. ___ 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
Re: [Freesurfer] (no subject)
Hi Meryem, it looks like it is looking for fingertap not fingertap.par. Could that be the problem? doug Meryem Ayse Yucel wrote: Hi, I am trying to use selxavg3-sess function and getting this error. Below is the error I get. I actually have this fingertap.par file but freesurfer somehow does not see it. Any help would be appreciated. Thanks! Meryem Yucel PMI Lab Extension format = nii.gz ERROR: opening /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/fingertap No such file or directory ??? Output argument partype (and maybe others) not assigned during call to /usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_ldpar4.m (fast_ldpar4). Error in == fast_ldpar4 at 45 par4 = []; Error in == flac_customize at 121 [par partype] = fast_ldpar4(parpath); Error in == fast_selxavg3 at 65 flac0 = flac_customize(flac0); ___ 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 ___ 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] Extraction of vertex identifiers from a significant cluster
Hi Florian, you can save the cluster as a label. This is a text file with xyz values for each vertex. The xyz values are in mni305 space. doug Florsek wrote: Dear all, We have performed a cluster analysis in Qdec and found a significant vertex-cluster after correction for multiple testing using the Monte Carlo simulation. Now, we would like to extract the (unique) identifiers of all vertices that form the significant cluster. We then would like to look up the spatial information (x, y, z) of these vertices. Our final aim is to map the vertices to an atlas which is different from that of Desikan. Is this a way suitable to achieve our aim? Many thanks for your help in advance! Best regards, Florian -- 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 ___ 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 mri_volcluster
Dear Doug, Can I run the mri_volcluter without --reg ? I am asking this because when I run: mri_glmfit-sim \ --glmdir GroupAnalysis_ADC.glmdir \ --grf 3 neg \ --cwpvalthresh .05 \ --overwrite gives me the following error (I also attached the log file): Also, does neg means now that Class1 (=controls) Class2 (=Patients) for my MD values? Many thanks. Antonella $Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Tue Feb 14 14:28:11 EST 2012 Linux EW-LNX3 2.6.32.26-175.fc12.x86_64 #1 SMP Wed Dec 1 21:39:34 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux elysa setenv SUBJECTS_DIR /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS FREESURFER_HOME /usr/local/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y GroupAnalysis-ADC-MASKED.ANAT+CVS-to-avg35.mgz --fsgd GroupAnalysis.fsgd dods --C contrast.mtx --glmdir GroupAnalysis_ADC.glmdir DoSim = 0 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 2.252995 mri_volcluster --in GroupAnalysis_ADC.glmdir/contrast/sig.mgh --mask GroupAnalysis_ADC.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_ADC.glmdir/contrast/grf.th3.neg.sig.cluster.mgh --sum GroupAnalysis_ADC.glmdir/contrast/grf.th3.neg.sig.cluster.summary --ocn GroupAnalysis_ADC.glmdir/contrast/grf.th3.neg.sig.ocn.mgh --cwpvalthresh .05 --seg fsaverage aparc+aseg.mgz --fwhmdat GroupAnalysis_ADC.glmdir/fwhm.dat --sign neg --thmin 3 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Using defalt ctab /usr/local/freesurfer/FreeSurferColorLUT.txt INFO: loading mask volume: GroupAnalysis_ADC.glmdir/mask.mgh INFO: MRIbinarize01(): nhits = 961260 Found 961260 voxels in mask ERROR: Input volume voxel dimensions do not match those in the registration file. If the input volume is in bshort/bfloat format, check that there is an accompanying bhdr file. grf.th3.neg.mri_glmfit-sim.log 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] Extraction of vertex identifiers from a significant cluster
You can do it in tksurfer using the Tools-CustomFill, then select fill to threshold (or something like that). I think there's a way to do it in QDEC too. Try looking at the tutorial. doug Florsek wrote: Hi Doug, do I have to manually draw the new label or can I somehow custom fill the cluster in tksurfer to create a label? Thank you for your quick answer! Florian Am 14.02.12 19:37, schrieb Douglas N Greve: Hi Florian, you can save the cluster as a label. This is a text file with xyz values for each vertex. The xyz values are in mni305 space. doug Florsek wrote: Dear all, We have performed a cluster analysis in Qdec and found a significant vertex-cluster after correction for multiple testing using the Monte Carlo simulation. Now, we would like to extract the (unique) identifiers of all vertices that form the significant cluster. We then would like to look up the spatial information (x, y, z) of these vertices. Our final aim is to map the vertices to an atlas which is different from that of Desikan. Is this a way suitable to achieve our aim? Many thanks for your help in advance! Best regards, Florian -- 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 ___ 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] (no subject)
Hi, Now it seems to be working with the par file but I am getting this error. Any help will be appreciated. Thanks, Meryem Computing compensation for resdual AR1 bias 1 -0.5 -0.473129(t=0.192235) 2 -0.25 -0.238292(t=1.09283) 3 0 -0.00411884(t=1.27811) 4 0.25 0.228971(t=2.16243) 5 0.5 0.459511(t=2.33787) AR1 Correction M: 0.00580007 1.07178 Computing contrast matrices OLS Beta Pass run 1t= 0.0 Global Mean Global In-Mask Mean = ??? Error using == mrdivide Matrix dimensions must agree. Error in == fast_selxavg3 at 399 RescaleFactor = flac0.inorm/gmean; Hi, I am trying to use selxavg3-sess function and getting this error. Below is the error I get. I actually have this fingertap.par file but freesurfer somehow does not see it. Any help would be appreciated. Thanks! Meryem Yucel PMI Lab Extension format = nii.gz ERROR: opening /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/fingertap No such file or directory ??? Output argument partype (and maybe others) not assigned during call to /usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_ldpar4.m (fast_ldpar4). Error in == fast_ldpar4 at 45 par4 = []; Error in == flac_customize at 121 [par partype] = fast_ldpar4(parpath); Error in == fast_selxavg3 at 65 flac0 = flac_customize(flac0); ___ 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] (no subject)
The mask used to compute the global mean does not have any voxels in it because the field of view is so small. Try running mkbrainmask-sess -s session -nero 1 -fsd bold Then run selxavg again. The above mkbrainmask command tells it to only erode the mask by one voxel (the default in preproc-sess is 3 which is removing all of them). doug Meryem Ayse Yucel wrote: Hi, Now it seems to be working with the par file but I am getting this error. Any help will be appreciated. Thanks, Meryem Computing compensation for resdual AR1 bias 1 -0.5 -0.473129(t=0.192235) 2 -0.25 -0.238292(t=1.09283) 3 0 -0.00411884(t=1.27811) 4 0.25 0.228971(t=2.16243) 5 0.5 0.459511(t=2.33787) AR1 Correction M: 0.00580007 1.07178 Computing contrast matrices OLS Beta Pass run 1t= 0.0 Global Mean Global In-Mask Mean = ??? Error using == mrdivide Matrix dimensions must agree. Error in == fast_selxavg3 at 399 RescaleFactor = flac0.inorm/gmean; Hi, I am trying to use selxavg3-sess function and getting this error. Below is the error I get. I actually have this fingertap.par file but freesurfer somehow does not see it. Any help would be appreciated. Thanks! Meryem Yucel PMI Lab Extension format = nii.gz ERROR: opening /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/fingertap No such file or directory ??? Output argument partype (and maybe others) not assigned during call to /usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_ldpar4.m (fast_ldpar4). Error in == fast_ldpar4 at 45 par4 = []; Error in == flac_customize at 121 [par partype] = fast_ldpar4(parpath); Error in == fast_selxavg3 at 65 flac0 = flac_customize(flac0); ___ 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 ___ 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] (no subject)
I tried this. It is still giving the same error. Should I check my mask files? Thanks. The mask used to compute the global mean does not have any voxels in it because the field of view is so small. Try running mkbrainmask-sess -s session -nero 1 -fsd bold Then run selxavg again. The above mkbrainmask command tells it to only erode the mask by one voxel (the default in preproc-sess is 3 which is removing all of them). doug Meryem Ayse Yucel wrote: Hi, Now it seems to be working with the par file but I am getting this error. Any help will be appreciated. Thanks, Meryem Computing compensation for resdual AR1 bias 1 -0.5 -0.473129(t=0.192235) 2 -0.25 -0.238292(t=1.09283) 3 0 -0.00411884(t=1.27811) 4 0.25 0.228971(t=2.16243) 5 0.5 0.459511(t=2.33787) AR1 Correction M: 0.00580007 1.07178 Computing contrast matrices OLS Beta Pass run 1t= 0.0 Global Mean Global In-Mask Mean = ??? Error using == mrdivide Matrix dimensions must agree. Error in == fast_selxavg3 at 399 RescaleFactor = flac0.inorm/gmean; Hi, I am trying to use selxavg3-sess function and getting this error. Below is the error I get. I actually have this fingertap.par file but freesurfer somehow does not see it. Any help would be appreciated. Thanks! Meryem Yucel PMI Lab Extension format = nii.gz ERROR: opening /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/fingertap No such file or directory ??? Output argument partype (and maybe others) not assigned during call to /usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_ldpar4.m (fast_ldpar4). Error in == fast_ldpar4 at 45 par4 = []; Error in == flac_customize at 121 [par partype] = fast_ldpar4(parpath); Error in == fast_selxavg3 at 65 flac0 = flac_customize(flac0); ___ 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 ___ 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] Question about hippocampal-subfield probability map
Dear experts, The hippocampal-subfield are expressed as probability maps. For each subfield, each voxel is assigned a probability of inclusion on a scale of [0-255]=[0-1]. However, If I were to select only voxels from each subfield's probability map corresponding to a 50% chance (i.e. mri_binarize -min 150), then I would expect that no subfield would overlap with another (i.e. a voxel shouldn't have greater than 50% probability of belonging CA1, AND a greater than 50% probability of belonging to CA4-DG. However it appears that this is not the case, and overlap does occur. Thus, unless I messed up, subfields are not mutually exclusive. Have I got this right? And if so, how do I obtain binary maps of subfields with no overlap? Thanks Josh ___ 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] Question about hippocampal-subfield probability map
Ha nevermind. While true, I can just mask the masks with each other and drop the over lapped regions. - Josh On Tue, Feb 14, 2012 at 3:59 PM, Joshua Lee jki...@ucdavis.edu wrote: Dear experts, The hippocampal-subfield are expressed as probability maps. For each subfield, each voxel is assigned a probability of inclusion on a scale of [0-255]=[0-1]. However, If I were to select only voxels from each subfield's probability map corresponding to a 50% chance (i.e. mri_binarize -min 150), then I would expect that no subfield would overlap with another (i.e. a voxel shouldn't have greater than 50% probability of belonging CA1, AND a greater than 50% probability of belonging to CA4-DG. However it appears that this is not the case, and overlap does occur. Thus, unless I messed up, subfields are not mutually exclusive. Have I got this right? And if so, how do I obtain binary maps of subfields with no overlap? Thanks Josh ___ 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] make average subject error
Hello, I have run into an error while trying to make an average subject using 200 scans. When I ran this command I got an error: *make_average_subject --xform talairach.xfm --out 200avgsub --subjects* The error: Allocing output mri_concat(40491) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 13726th slice Cannot allocate memory WARNING: could not create average segmentation for aseg ... ... but continuing make_average_volume done The average sub folder does not contain aseg.mgz and p.aseg.mgz files. *The version of Freesurfer I am using:* v 1.313.2.6 2010/08/04 15:50:56 nicks *My memory:* 8 GB 1333 MHz DDR3 *Hard-drive:* 276.49 GB free MAC OS X v 10.6.8 I have scoured the archives for the answer to my question to no avail. All of the answers before seemed to revolve around versions of Freesurfer which I expect were updated. Nick Schmanksy wrote sorry, i meant to say include the --no-aseg flag with make_average_volume (make_average_subject is just a wrapper script that calls make_average_volume and make_average_surface). But wouldn't this prevent segmentation? Is there a way to then add segmentation after? Sorry if these are novice questions (as I am a novice). Thank you, Adam ___ 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] TRACULA question: pathstats.byvoxel.txt
Hello Tracula Developer User, I found a few subjects have pathstat.overall.txt information but with blank voxel information in pathstats.byvoxel.txt. For such tracts, they usually len_min = len_max = len_avg. Anyone know what happened for the fiber tracking? Is it possible to extract the byvoxel information along the tract? Thanks, Minjie For example: [minjiewu@ccmfsl1 data]$ more 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt # Title Pathway Statistics # # generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats # cvs_version # cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr --dtbase /ccm/pavuluri/rest/DTI/data/223 31/dmri/dtifit --path rh.slfp --subj 22331 --out /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt --outvox /ccm/pavuluri/rest/DTI/data/ 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.byvoxel.txt # sysname Linux # hostname ccmfsl2.psych.uic.edu # machine x86_64 # user minjiewu # anatomy_type pathway # # subjectname 22331 # pathwayname rh.slfp # Count 1000 Volume 86 Len_Min 86 Len_Max 86 Len_Avg 86 Len_Center 0 AD_Avg 0.00112029 AD_Avg_Weight 0.00112029 AD_Avg_Center nan RD_Avg 0.000783836 RD_Avg_Weight 0.000783836 RD_Avg_Center nan MD_Avg 0.000895987 MD_Avg_Weight 0.000895987 MD_Avg_Center nan FA_Avg 0.264347 FA_Avg_Weight 0.264347 FA_Avg_Center nan ___ 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] Question about hippocampal-subfield probability map
That is, I can use fslmaths from fsl suite to subtract my binarized subfield rois. - Josh On Tue, Feb 14, 2012 at 4:58 PM, Joshua Lee jki...@ucdavis.edu wrote: Ha nevermind. While true, I can just mask the masks with each other and drop the over lapped regions. - Josh On Tue, Feb 14, 2012 at 3:59 PM, Joshua Lee jki...@ucdavis.edu wrote: Dear experts, The hippocampal-subfield are expressed as probability maps. For each subfield, each voxel is assigned a probability of inclusion on a scale of [0-255]=[0-1]. However, If I were to select only voxels from each subfield's probability map corresponding to a 50% chance (i.e. mri_binarize -min 150), then I would expect that no subfield would overlap with another (i.e. a voxel shouldn't have greater than 50% probability of belonging CA1, AND a greater than 50% probability of belonging to CA4-DG. However it appears that this is not the case, and overlap does occur. Thus, unless I messed up, subfields are not mutually exclusive. Have I got this right? And if so, how do I obtain binary maps of subfields with no overlap? Thanks Josh ___ 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] recon-all error (nu_correct problem)
Hello, Freesurfers, I got an error message when I trying to use recon-all function in freesurfer on the XUbuntu system installed on the VirtualBox on a Windows 7 machine. I searched the e-mailing list but I can't find any answers. My problem is related to the nu_correct and nu_estimate_np_and_em. However, nu_correct and nu_estimate_np_and_em were located to exact path (/home/virtualuser/freesurfer/mni/bin). echo $MNI_DATAPATH, echo $MNI_PERL5LIB showed exact path. In addition, I already tried to use fixup_mni_paths. Could anyone give me an advice for fixing up this problem? Thanks in advance. Cheers, EK error message! #@# Nu Intensity Correction Wed Feb 15 01:23:24 EST 2012 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/virtualuser/Desktop/DATA/30664304/mri /home/virtualuser/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux Wed Feb 15 01:23:25 EST 2012 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 tmpdir is ./tmp.mri_nu_correct.mni.17682 /home/virtualuser/Desktop/DATA/30664304/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17682/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17682/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.17682/nu0.mnc... Iteration 1 Wed Feb 15 01:23:37 EST 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.17682/nu0.mnc ./tmp.mri_nu_correct.mni.17682/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17682/0/ [virtualuser@FreeSurfer:/home/virtualuser/Desktop/DATA/30664304/mri/] [2012-02-15 01:23:37] running: /home/virtualuser/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17682/0/ ./tmp.mri_nu_correct.mni.17682/nu0.mnc ./tmp.mri_nu_correct.mni.17682/nu1.imp Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux ___ 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.
