[Freesurfer] preproc-sess error with -per-session flag
Dear Freesurfers, I ran into an issue while trying to preprocess some resting state data. As I wished to use the first slice to correct for motion, I typed in this command : preproc-sess -s 5167/ -fsd bold -stc down -surface fsaverage lhrh -mni305-2mm -fwhm 6 -*per-session. * The error message was the following : .. stc-sess Done 5167 To Surface - rawfunc2surf-sess -fwhm 6 -s 5167 -d /Applications/freesurfer/sessions -fsd bold -stc down -update instem fmcpr.down outstem fmcpr.down.sm6.fsaverage.hemi -- 1/1 5167 1/1 5167 007 lh - Fri Nov 25 09:39:53 CET 2011 ERROR: could not determine file for /Applications/freesurfer/sessions/5167/bold/007/fmcpr.down When I use the middle slice as a reference slice with the command *-per-run *I don't have any problems. Does any one know where this is coming from? I see some people already had the same issue a while ago, does any one know if a solution was found? Cheers, Elisa Scariati ___ 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] Yeo_JNeurophysiol11_FreeSurfer networks
Hi Thomas, Thank you for your answer, I will try to project your parcellation in fsaverage space to BASGU space first. Regards, Yolanda 2011/11/26 Thomas Yeo yeoye...@gmail.com Hi Yolanda, Just to understand what you are doing, you have run BASGU through recon-all and you are trying to project the surface parcellation into the anatomical volume of BASGU? The annotation we are providing is actually in fsaverage space, so you need to first project the parcellation from fsaverage space to BASGU native surface space before running mris_annot_to_segmentation to project the parcellation into his/her anatomical volume. To project the parcellation from freesurfer surface space to the subject's native surface space, I think you can use mri_surf2surf, although I am not sure if there's a more specific freesurfer function that is specialized for transferring annotation files. --Thomas On Thu, Nov 24, 2011 at 4:11 PM, Yolanda Vives yvi...@pic.es wrote: Dear Freesurfer experts, I would like to use the Yeo_JNeurophysiol11_FreeSurfer parcellations with my dataset and I am not sure what I have to do. I have used the mris_annot_to_segmentation command but I have the following error: mris_annot_to_segmentation BASGU lh inflated ./fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot ../Yeo_JNeurophysiol11_MNI152/Yeo2011_17Networks_ColorLUT.txt test reading /freesurfer/BASGU/surf/lh.inflated... reading colortable from annotation file... colortable with 18 entries read (originally MyColorLUT) mri_read(): couldn't determine type of file /freesurfer/BASGU/mri/T1 (null): could not read T1 for template volume I have a T1.mgz file inside mri/. Where could be the problem? Is this command appropriate? Thank you in advance, Yolanda ___ 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] Number of maximal permutations / pooled variance estimates
Dear FS experts I have a question regarding the number of maximal permutations. I compare a single patient versus a group of six control subjects. Intuitively, I guess that only six different permutations are possible. However, when running 100 permutations in FS with mri_glmfit-sim, I get different results for each permutations as confirmed in the CSD file. So, I am not sure any longer whether the permutations are built by permuting the subjects or anything else. The other question is how mri_glmfit estimates the variance. Because I have only one subject in the patient group, there is not variance in that group and therefore I guess mri_glmfit used pooled (across both groups) estimates of variance, isn't it? Any comment is highly appreciated Thanks in advance Best regards Jürgen Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ 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] longitudinal processing edema from lesion causing skewed registration
Hi, I am doing longitudinal processing of multiple subjects (each with 3 sessions) post stroke. However, some of the lesions are so extensive in the first session that they cause edema and push the brain midline. This greatly affects the pial surface on the lesioned hemishpere after longitudinal processing with the other sessions of the same subject. Is there anyway to fix this without manually editing the area? Would it help to register each session individually to fsaverage instead of registering them first across sessions? Thank you! Kelsi ___ 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] running recon-all after editing aseg.mgz
If you only made edits to the aseg, then you can run: recon-all -s subject_name -autorecon2-aseg -autorecon3 which omits some stages that don't need to be redone (but which would otherwise be included if you use the -autorecon2 flag). If you in addition added control points, then you would run recon-all -s subject_name -autorecon2-cp -autorecon3 which includes the stages needed to handle the aseg edits as well. cheers, -MH On Fri, 2011-11-25 at 22:49 +0100, Tetiana Dadakova wrote: Hi Maria, Yes, you are editing aseg.mgz. After saving the segmentation, you should run recon-all -s subject_name -autorecon2 -autorecon3. If you also added some control points, then you should run recon-all -s subject_name -autorecon2-cp -autorecon3 Best wishes, Tanja. On Fri, Nov 25, 2011 at 10:40 PM, Maria Jalbrzikowski mjalbrzikow...@gmail.com wrote: Hi, I am a relatively new user of Freesurfer and have a couple questions. I have gone through the tutorials and I am now at the point where I check the segmentation. If I open my subject in tkemdit (tkmedit your_subject_name brainmask.mgz -surfs -aseg) and use the edit the segmentation and then press save segmentation, I am editing the aseg.mgz file, correct? After doing that, what parts of recon-all would I need to run again? Thanks, Maria -- Maria Jalbrzikowski, M.A. University of California, Los Angeles ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] subjects with contrast medium
do you mean gado? If so, it should work although things like dura and choroid that get very bright may need some extra manual editing. cheers Bruce On Mon, 28 Nov 2011, LAOUCHEDI MAKHLOUF wrote: hi everyone i am working on traumatic brain injury and noticed that some exams i received recently (T1datasets) were conducted using à contrast medium: sometimes the whole memisphere presents hypersignal. can i run recon-all (if there is a way) on such subjects? thanks ___ 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] Surface X, Y, Z to Tailarach or Volume Index
Dear all, I wrote my own function to show the 3D surfaces in Matlab, works splendidly. I now however want to be able to point out Tailarach/MNI coordinates on the 3D surface. I however only have the x, y, z format that is saved in the asc files, which is just where a certex is located in space, with no relation to the original brain whatsoever. The only thing I can retrieve is the vertex index (because that's in the asc file). How can convert the 3D X, Y, Z values (the same values you get in the console if you click on a point on the surface in tksurfer) to either Vertex RAS/Talairach or Volume index? I read the information on conversions between surface Talairach and Volume Index, that works, but this case is different: I am actually referring to the 3D locations of the vertices. Hopefully someone can help me, thanks a lot in advance, best, Frank ___ 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 projecting vector results for segmented cortical regions
hello we are trying to project a vector of results for segmented cortical regions (i.e.,... lh_middletemporal_thickness 0.000757119 rh_middletemporal_thickness 8.06E-05 lh_parahippocampal_thickness -0.000510407 rh_parahippocampal_thickness 0.000625997 lh_pericalcarine_thickness 0.000499749 rh_pericalcarine_thickness 0.000903678 lh_superiortemporal_thickness 0.001732855 rh_superiortemporal_thickness 0.000184256 lh_temporalpole_thickness 0.001075362 rh_temporalpole_thickness -0.000381165 lh_transversetemporal_thickness 0.000558122 rh_transversetemporal_thickness 6.65E-05 ...) however, we are unsure of how to do this. so, our question is— what is the sequence of steps we need to take to visualize our results on the segmented 3D template in tksurfer. Thanks for your help, Brian Weisinger ___ 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 projecting vector results for segmented cortical regions
Thanks for the help. We don't have matlab here in our lab, but we do have R. Is there a way to use R and get the same desired result? On 11/28/11 11:46 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brian, I guess you can use read_annotation.m in matlab and set every vertex within the given parcellation to the value you specify below, then write it out as either an nvertices x 1 x 1 .mgz file with save_mgh, or use write_curv.m cheers Bruce On Mon, 28 Nov 2011, Weisinger, Brian (NIH/NIMH) [F] wrote: hello we are trying to project a vector of results for segmented cortical regions (i.e.,... lh_middletemporal_thickness 0.000757119 rh_middletemporal_thickness 8.06E-05 lh_parahippocampal_thickness -0.000510407 rh_parahippocampal_thickness 0.000625997 lh_pericalcarine_thickness 0.000499749 rh_pericalcarine_thickness 0.000903678 lh_superiortemporal_thickness 0.001732855 rh_superiortemporal_thickness 0.000184256 lh_temporalpole_thickness 0.001075362 rh_temporalpole_thickness -0.000381165 lh_transversetemporal_thickness 0.000558122 rh_transversetemporal_thickness 6.65E-05 ...) however, we are unsure of how to do this. so, our question is? what is the sequence of steps we need to take to visualize our results on the segmented 3D template in tksurfer. Thanks for your help, Brian Weisinger ___ 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
[Freesurfer] Surface Area from mri_surfcluster versus mri_segstats
I've noticed that if I run mri_surfcluster to produce a label file, then merge the labels into a single label using mri_mergelabels, then mri_segstats with the slabel option with the fsaverage subject; I get different surface areas from mri_surfcluster (summed all the cluster areas) and mri_segstats (1 area). Is there something wrong with my implementation of these three commands or is it expected that the two methods would produce different values? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School 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. ___ 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] create an annotation file
hi everyone i am new in freesurfer and i want to create a masque of some color made of somme régions labels (say for ex. the post central gyrus and precentral gyrus or any combination of geri and sulcus) to put it as a layer on an a pial or inflated surface. how can i proceed? thanks ___ 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] Installation FS
Dear FreeSurfer Group I have some problem for installing the FS. Using following links, I downloaded and installed freesurfer-Darwin-leopard. For next step, in terminal when I write source $FREESURFER_HOME/SetUpFreeSurfer.sh or source $FREESURFER_HOME/SetUpFreeSurfer.csh it says that No such file or directory while I can see both in freesurfer folder. Can you please guide me what is the reason and how I can solve it. http://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration -- Best Regards --- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * * ___ 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 Error: bvecs and bvals don't have the same number of entries
Sorry for the delay in responding, I wanted to try every permutation that I could think of. I updated the tracula binaries for snow leopard (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019946.html) and that gives me some of the same, and some different issues that may help. First, if the bvec file is in the correct format (3 columns), then it copies the file correctly and trac-all continues smoothly. If the file is in the 3 row format (needing to be transposed), then tracula will only copy the first 9 numbers out of it giving the error of not having the correct number of bvecs to bvals. So that seems fixable, I just need to reorient all of our bval and bvec files into the correct format. I'm still a bit unsure why tracula won't create the bvec and bval files during the mri_convert stage. I have been using dcm2nii to create these two files but then continue to give tracula the path to the dicom files. So the orientation of this file could be related to how dcm2nii writes the files. Any suggestions would be very welcome. As it stands, my current workflow is: 1. use dcm2nii to create bvec and bval files 2. reorient bvec and bval files to be 3 column and 1 column format respectively. 3. run trac-all -prep with a config file showing where the dicom images are and hand specifying the bvec and bval files Peter Peter J. Molfese, Ph.D. Postdoctoral Associate Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 peter.molf...@yale.edu CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intende d recipient, please contact the sender immediately by reply e-mail and destroy all copies of the original message. ___ 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 Error: bvecs and bvals don't have the same number of entries
Hi Peter - The format for the bvec and bval files is explained in: $FREESURFER_HOME/bin/dmrirc.example If you've structured your dmrirc following this example file and you're still getting this error, please send the following so I can debug this: - your exact trac-all command line - your dmrirc file - your trac-all.log - the actual bvecs and bvals files that you specify in your dmrirc Thanks, a.y On Mon, 28 Nov 2011, Peter J. Molfese wrote: Sorry for the delay in responding, I wanted to try every permutation that I could think of. I updated the tracula binaries for snow leopard (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019946.html) and that gives me some of the same, and some different issues that may help. First, if the bvec file is in the correct format (3 columns), then it copies the file correctly and trac-all continues smoothly. If the file is in the 3 row format (needing to be transposed), then tracula will only copy the first 9 numbers out of it giving the error of not having the correct number of bvecs to bvals. So that seems fixable, I just need to reorient all of our bval and bvec files into the correct format. I'm still a bit unsure why tracula won't create the bvec and bval files during the mri_convert stage. I have been using dcm2nii to create these two files but then continue to give tracula the path to the dicom files. So the orientation of this file could be related to how dcm2nii writes the files. Any suggestions would be very welcome. As it stands, my current workflow is: 1. use dcm2nii to create bvec and bval files 2. reorient bvec and bval files to be 3 column and 1 column format respectively. 3. run trac-all -prep with a config file showing where the dicom images are and hand specifying the bvec and bval files Peter Peter J. Molfese, Ph.D. Postdoctoral Associate Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 peter.molf...@yale.edu CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intende d recipient, please contact the sender immediately by reply e-mail and destroy all copies of the original message. ___ 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] FSGD for dtrecon group analysis
Hi Antonella, 1) I will be very grateful if you let me know what data I should use for my fsgd when I run the GLM group analysis: the dti data after running the dtrecon (for example for my first control I called this directory C01_dti or the FS data after running recon-all on the structural data in this case called C01? Given that you are preparing your fa data for the analysis, indicated below, you will need to use the dti directories, eg.: C01_dti. 2) When I concatenate fa from individuals into one file using: mri_concat */fa-tal.nii --o group-fa-tal.nii how I can check if the order agrees with my fsgd? You can list the files using ls -l */fa-tal.nii and the order that you see is the order in which they get concatenated in your output file. You need to make sure that that order agrees with the contents of your fsgd file. 3) When I concatenate fa from individuals into one file do I need to move all the fa-tal.nii into one directory or I can have each of the fa-tal files under different subject's directory? Aas example: C01_dti will contain the corresponding fa-tal.nii for the control 1, C02_dti will contain his corresponding fa-tal.nii, etc and all the subjects C01_dti, C02_dti,...P01_dti, P02_dti... are located into one directory called dtrecon. You can have them under different subdirectories, but then your mri_concat command needs to reflect that, for example, mri_concat */dtrecon/fa-tal.nii --o group-fa-tal.nii --Lilla___ 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] Installation FS
Hi Nooshin, Did you include the full path to your freesurfer directory when setting the FREESURFER_HOME variable with the 'setenv' command? -Louis On Mon, 28 Nov 2011, nooshin n.zade wrote: Dear FreeSurfer Group I have some problem for installing the FS. Using following links, I downloaded and installed freesurfer-Darwin-leopard. For next step, in terminal when I write source $FREESURFER_HOME/SetUpFreeSurfer.sh or source $FREESURFER_HOME/SetUpFreeSurfer.csh it says that No such file or directory while I can see both in freesurfer folder. Can you please guide me what is the reason and how I can solve it. http://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration ___ 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 projecting vector results for segmented cortical regions
If you've got any Python users in the lab, this shouldn't be to hard to accomplish with pysurfer: pysurfer.github.com I'm happy to walk you through the steps if you're interested. Michael On Mon, Nov 28, 2011 at 8:52 AM, Weisinger, Brian (NIH/NIMH) [F] brian.weisin...@nih.gov wrote: Thanks for the help. We don't have matlab here in our lab, but we do have R. Is there a way to use R and get the same desired result? On 11/28/11 11:46 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brian, I guess you can use read_annotation.m in matlab and set every vertex within the given parcellation to the value you specify below, then write it out as either an nvertices x 1 x 1 .mgz file with save_mgh, or use write_curv.m cheers Bruce On Mon, 28 Nov 2011, Weisinger, Brian (NIH/NIMH) [F] wrote: hello we are trying to project a vector of results for segmented cortical regions (i.e.,... lh_middletemporal_thickness 0.000757119 rh_middletemporal_thickness 8.06E-05 lh_parahippocampal_thickness -0.000510407 rh_parahippocampal_thickness 0.000625997 lh_pericalcarine_thickness 0.000499749 rh_pericalcarine_thickness 0.000903678 lh_superiortemporal_thickness 0.001732855 rh_superiortemporal_thickness 0.000184256 lh_temporalpole_thickness 0.001075362 rh_temporalpole_thickness -0.000381165 lh_transversetemporal_thickness 0.000558122 rh_transversetemporal_thickness 6.65E-05 ...) however, we are unsure of how to do this. so, our question is? what is the sequence of steps we need to take to visualize our results on the segmented 3D template in tksurfer. Thanks for your help, Brian Weisinger ___ 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 ___ 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.
