[Freesurfer] A Question Regarding Topology Correction
External Email - Use Caution Dear Bruce, The other day I asked you about doing topology correction on my own segmentation(I have put my first e-mail and you response in the following so u can track easier). according to what you suggested, I have created a synthetic T1 volume based on my own segmentation. Now I wonder what to do exactly as the second step. Should I use "mris_fix_topology"? I would be grateful if you could help me with that. Best, Maedeh "Dear FreeSurfer experts, I know that FreeSurfer does segmentation, surface reconstruction and topology correction through its routine pipeline using "recon-all" . However, I have some T2w brain MR images and I have done the segmentation and extracted WM, GM, and CSF with my own algorithm. Now I need to remove back to back (i.e. a part of topology correction) which is caused in sulci due to the segmentation. In other word, after doing my segmentation, I wanna open the closed concavities in CSF that were open originally. Now I wanna know if I can do the topology correction using FreeSurfer while I have done the segmentation by myself? I would be grateful if you could help me with that. Best, Maedeh Hi Maedeh in principle you can, although it would be a lot easier if you just had a reasonable quality T1. If not, you will need to create all the files that recon-all expects to exist prior to the topology correction step (wm.mgz, norm.mgz, orig.mgz, ). Maybe the easiest thing to do would be to use your gray/white/csf segmentation to create a synthetic T1 volume? Set all the wm voxels to 110, all the gray to 70 and all the csf to 20, or something like that? cheers Bruce"___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: A Question Regarding Topology Correction
External Email - Use Caution From: "Maedeh Khalilian" To: "freesurfer@nmr.mgh.harvard.edu" Date: Thu, 11 Jul 2019 07:37:05 +0430 Subject: A Question Regarding Topology Correction Dear FreeSurfer experts, I know that FreeSurfer does segmentation, surface reconstruction and topology correction through its routine pipeline using "recon-all" . However, I have some T2w brain MR images and I have done the segmentation and extracted WM, GM, and CSF with my own algorithm. Now I need to remove back to back (i.e. a part of topology correction) which is caused in sulci due to the segmentation. In other word, after doing my segmentation, I wanna open the closed concavities in CSF that were open originally. Now I wanna know if I can do the topology correction using FreeSurfer while I have done the segmentation by myself? I would be grateful if you could help me with that. Best, Maedeh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] A Question Regarding Topology Correction
External Email - Use Caution Dear FreeSurfer experts, I know that FreeSurfer does segmentation, surface reconstruction and topology correction through its routine pipeline using "recon-all" . However, I have some T2w brain MR images and I have done the segmentation and extracted WM, GM, and CSF with my own algorithm. Now I need to remove back to back (i.e. a part of topology correction) which is caused in sulci due to the segmentation. In other word, after doing my segmentation, I wanna open the closed concavities in CSF that were open originally. Now I wanna know if I can do the topology correction using FreeSurfer while I have done the segmentation by myself? I would be grateful if you could help me with that. Best, Maedeh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] A Question Regarding the Command "mris_divide_pacellation"
External Email - Use Caution Dear Bruce, Thank u very much for replying. sorry I'm still a little bit doubtful, just as a confirmation: by repeatable you mean I can repeat it and every time get a a new result? or every time the result will be the same? Best, Maedeh, Hi Maedeh I think it divides along the maximum variance eigen-axis, so should be repeatable. cheers Bruce On Thu, 6 Jun 2019, Maedeh Khalilian wrote: > > External Email - Use Caution > > Dear experts, > I use the file "lh/rh.aparc.annot" and a splitfile as the inputs of?the command > "mris_divide_parcellation" in order to have a parcellation with more regions. > Now I have a question: for example if in my splitfile I write 4 in front of the region "precuneus", > how does it divide this region?into 4 subregions? Is it based on a specific pattern or it is random? > I mean if I?repeat this command line 100 times with the same splitfile, will?the results be the > same??I would be grateful if you could help me. > Best regards, > Maedeh,___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] A Question Regarding the Command "mris_divide_pacellation"
External Email - Use Caution Dear experts, I use the file "lh/rh.aparc.annot" and a splitfile as the inputs of the command "mris_divide_parcellation" in order to have a parcellation with more regions. Now I have a question: for example if in my splitfile I write 4 in front of the region "precuneus", how does it divide this region into 4 subregions? Is it based on a specific pattern or it is random? I mean if I repeat this command line 100 times with the same splitfile, will the results be the same? I would be grateful if you could help me. Best regards, Maedeh, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] A Question Regarding Smoothing a Surface
External Email - Use Caution Dear experts, I have a parcellation scheme (an annotation file). Now I wanna smooth the map for better visualization. The command "mri_surf2surf" can do it ,but it doesn't recognize .annot. Now I wonder how to do it. I would appreciate it if u could help me with that. Best wishes, Maedeh, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: Visualizing Volumetric Files on Surface
External Email - Use Caution > From: "Maedeh Khalilian" > To: "freesurfer@nmr.mgh.harvard.edu" > Date: Thu, 09 May 2019 01:24:58 +0430 > Subject: Visualizing Volumetric Files on Surface > Dear FreeSurfer experts; > I have created some volumetric(.nii) files in FreeSurfer (the procedure > is > as following: lh/rh.aparc.annot> mri_divide_parcellation > > mri_aparc2aseg > > deleting subcortical and white matter regions in order to keep just > cortical > regions on GM). > > Now I wanna visualize my volumetric files on surface so that I myself > can > determine the color of each region. But I dunno how to do it exactly. > I would be grateful if u could help me with that. > Thanks in advance > Best regards > Maedeh, > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Visualizing Volumetric Files on Surface
External Email - Use Caution Dear FreeSurfer experts; I have created some volumetric(.nii) files in FreeSurfer (the procedure is as following: lh/rh.aparc.annot> mri_divide_parcellation > mri_aparc2aseg > deleting subcortical and white matter regions in order to keep just cortical regions on GM). Now I wanna visualize my volumetric files on surface so that I myself can determine the color of each region. But I dunno how to do it exactly. I would be grateful if u could help me with that. Thanks in advance Best regards Maedeh, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Excluding Specific Regions from a Volumetric File
External Email - Use Caution Dear FreeSurfer experts, I have used "mri_aparc2aseg" in order to map my parcellation file to a volumetric file, but in the end I wanna exclude some regions which I know their labels. I think it must be opposite of what "mri_binarize" does. I wonder how to do that. I would be grateful if u could help me with that. Best regards, Maedeh___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Excluding Specific Regions from a Volumetric File
External Email - Use Caution Dear FreeSurfer experts, I have used "mri_aparc2aseg" in order to map my parcellation file to a volumetric file, but in the end I wanna exclude some regions which I know their labels. I think it must be opposite of what "mri_binarize" does. I wonder how to do that. I would be grateful if u could help me with that. Best regards, Maedeh___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Increasing the Number of a non-FreeSurfer Parcellation
External Email - Use Caution Dear Bruce The parcellation I have is not on surface, it is volumetric. I wanna increase the number of its ROIs, I thought maybe I can change it into an annotation file and then use "mris_divide_parcellation". Hope it is clear enough now. Best Maedeh___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Increasing the Number of a non-FreeSurfer Parcellation
External Email - Use Caution Dear experts, I have a question, if I have a parcellation which is not the output of FreeSurfer, can i increase the number of its parcels in FreeSurfer? Maybe if I can change my file into an annotation file is it possible? I would be grateful if u could help me. Cheers, Maedeh. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Necessity of Matlab for Using FsFast
External Email - Use Caution Dear experts, Is it necessary to install Matlab to use FsFast for functional connectivity? Thanks in advance Best Maedeh,___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Registering Anatomical Parcellation to DWI
External Email - Use Caution Dear FreeSurfer experts, I have a parcellation and a whole brain white matter files which are the outputs of FreeSurfer. I want to register them to my DWI. I mean I want my parcellation and white matter to be in the physical space of my DWI. Can FreeSurfer do it for me? If not , can you suggest me a toolbox that can do it fast? I would be grateful if u could help me. Cheers, Maedeh,___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem in Installing FreeSurfer on Mint19
External Email - Use Caution Dear Tim, I did it successfully, Thanks more... Best Maedeh___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem in Installing FreeSurfer on Mint19
External Email - Use Caution Dear experts, Thank u very much for all the help so far I have mint19 on my system and I have installed FreeSurfer on it. when I run a command like "mri_convert" it is ok. But when I run "recon-all" and some other commands, I see the error below : bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory by the way my default setup file is .bashrc. I really dunno what the problem is.I would be grateful if u could help me. Cheers, Maedeh___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Installing Two Versions of FreeSurfer on One System at the Same Time
External Email - Use Caution Dear FreeSurfer experts, I wonder if I can install two versions of FreeSurfer (the latest one and an older one) on one system at the same time. Thanks more. Best Maedeh,___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Functional Connectivity in FreeSurfer
External Email - Use Caution Dear FreeSurfer experts, I have a general question, if i have a parcellation(an annotation file e.g aparc.annot which is the output of FreeSurfer) is FreeSurfer able to calculate the functional connectivity between the regions(parcels) using rs-fMRI data? I mean can I have a 68*68 matrix showing the functional connectivity between each pair of regions(parcels) at the end? I would be grateful if u could help me. best regards, Maedeh___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] using mris_ca_train
External Email - Use Caution Dear Freesurfer experts, I have a question, does the number of input subjects matter in using "mris_ca_train" or not? i mean does it affect the results?(maybe the more subjects, the better result) and if yes, what is an approximate number? and the second question is that if there is a way so i can check my .gcs file? for example for reading annotation files u had an m file named "read_annotation.m".it did help me alot. Generally how can i check my .gcs file and evaluate its quality? just by applying it on a subject by "mris_ca_label" ? i really appreciate you if you can help me, Kind regards, Maedeh, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] very bad result using "mris_ca_train" and "mris_ca_label"
External Email - Use Caution Dear Dr.Bruce Fischl Thank you very much for your great sense of responsibility. Sure, i have sent you a zip file named "Maedeh_results"(it was a rather big sized one so i had to send it through Wetranser). Hope you have received it. However, a general question is that, according to freesurfer help the required arguments for "mris_ca_train" are : mris_ca_train [options] ... as it seems it gets one surf file(e.g sphere.reg),and one annotation file, but several subjects...so what does this surface file refer to?should i make an average of all subjects' .reg files? and also for the annotation file ! just one .annot is enough or i have to make an average of several annotation files? if yes, how should i do that? i would be grateful if you could help me. Best regards Maedeh,___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] very bad result using "mris_ca_train" and "mris_ca_label"
External Email - Use Caution Dear Freesurfer experts, I am using "mris_divide_parcellation" in order to increase the region numbers of Freesurfer parcellation output using "recon-all". e.g i have a 200-region parcellation.Now i wanna use "mris_ca_train" and this .annot file as an input to create an atlas file(.gcs). The code i run and the results on the terminal are : $ mris_ca_train lh sphere.reg LDestrieux200 test1 $SUBJECTS_DIR/test1/label/lh.Destrieux200.gcs computing means for 1 subject processing subject test1, 1 of 1... reading colortable from annotation file... colortable with 261 entries read (originally none) 4210 classifier means computed, 1.6/vertex, 0.5 priors/vertex computing covariances for 1 subject processing subject test1, 1 of 1... reading colortable from annotation file... colortable with 261 entries read (originally none) 75009 holes filled in class prior array 0 holes filled in gcsan array writing classifier array to /home/user/Desktop/Maedeh/test1/label/lh.Destrieux200.gcs... classifier array training took 0 minutes and 4 seconds. the problem is that when i use "lh.Destrieux200.gcs" and "mris_ca_label" to create an annotation file, the result i have is kinda awful !! and when i check it by tksurfer , the parcellation is not complete and i just see few regions...i dunno where i am making a mistake. the code and the results on terminal are : mris_ca_label test1 lh sphere.reg lh.Destrieux200.gcs $SUBJECTS_DIR/test1/label/lh.myDestrieux200.annot $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from lh.Destrieux200.gcs... average std = 0.2 using min determinant for regularization = 0.000 0 singular and 570 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000:479 changed, 114679 examined... 001: 18 changed, 2844 examined... 002: 1 changed, 89 examined... 003: 0 changed, 5 examined... 000: 241 total segments, 38 labels (248 vertices) changed 001: 203 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) writing output to /home/user/Desktop/Maedeh/test1/label/lh.myDestrieux200.annot... classification took 0 minutes and 3 seconds. I would be grateful if u could help me. Cheers, Maedeh,___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] very bad result using "mris_ca_train" and "mris_ca_label"
External Email - Use Caution Dear Freesurfer experts, I am using "mris_divide_parcellation" in order to increase the region numbers of Freesurfer parcellation output using "recon-all". e.g i have a 200-region parcellation.Now i wanna use "mris_ca_train" and this .annot file as an input to create an atlas file(.gcs). The code i run and the results on the terminal are : $ mris_ca_train lh sphere.reg LDestrieux200 test1 $SUBJECTS_DIR/test1/label/lh.Destrieux200.gcs computing means for 1 subject processing subject test1, 1 of 1... reading colortable from annotation file... colortable with 261 entries read (originally none) 4210 classifier means computed, 1.6/vertex, 0.5 priors/vertex computing covariances for 1 subject processing subject test1, 1 of 1... reading colortable from annotation file... colortable with 261 entries read (originally none) 75009 holes filled in class prior array 0 holes filled in gcsan array writing classifier array to /home/user/Desktop/Maedeh/test1/label/lh.Destrieux200.gcs... classifier array training took 0 minutes and 4 seconds. the problem is that when i use "lh.Destrieux200.gcs" and "mris_ca_label" to create an annotation file, the result i have is kinda awful !! and when i check it by tksurfer , the parcellation is not complete and i just see few regions...i dunno where i am making a mistake. the code and the results on terminal are : mris_ca_label test1 lh sphere.reg lh.Destrieux200.gcs $SUBJECTS_DIR/test1/label/lh.myDestrieux200.annot $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from lh.Destrieux200.gcs... average std = 0.2 using min determinant for regularization = 0.000 0 singular and 570 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000:479 changed, 114679 examined... 001: 18 changed, 2844 examined... 002: 1 changed, 89 examined... 003: 0 changed, 5 examined... 000: 241 total segments, 38 labels (248 vertices) changed 001: 203 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 7 changed) writing output to /home/user/Desktop/Maedeh/test1/label/lh.myDestrieux200.annot... classification took 0 minutes and 3 seconds. I would be grateful if u could help me. Cheers, Maedeh,___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Seeing the Results in the Original Space
External Email - Use Caution Dear FreeSurfer Experts, How can i have the results of FreeSurfer in its original space? The results have rotation and also the axial and the coronal images are replaced with each other. Thanks in advance Best regards, Maedeh___ 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] A Question about Estimating the Cortical Thickness for Each Subregion
External Email - Use Caution Dear Dr.Bruce Fischl, Thanks for helping me, actually in other words, i am gonna make my brain network based on the graph theory, the nodes of my graph are the parcels and for the edges between the nodes i am gonna compute the cortical thickness or maybe another measurment of the subregions and correlate them for each pair to find the edges and their weights. Hope I've explained clearly. Kind regards, Maedeh, ___ 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] A Question about Estimating the Cortical Thickness for Each Subregion
External Email - Use Caution Dear Freesurfer Experts; I have a question, are there any ways in FreeSurfer to estimate the gray matter volume or cortical thickness of each region after parcellation, in order to define the edges in the brain network? Kind regards, Maedeh,___ 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] Saving the Results into the Original Space
External Email - Use Caution Dear FreeSurfer experts, How can I save the result of parcellation and segmentation into the original space? I would appreciate any help. Best regards, Maedeh___ 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] Seeing Parcels as volumes
External Email - Use Caution Dear Douglas Greve; Thank you for your great help.I did what you said successfully.Now I have another question. I have used "mri_divide_parcellation" to have more parcels.this command gives me a ".annot" file.How can i change this file into a format such as .nii so i can see the volumes in Mricro? Cheers Maedeh,___ 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] Seeing the Parcels as Volumes
External Email - Use Caution Dear FreeSurfer experts, I have used "mri_annnotation2label" and "mri_label2vol" to change the parcellation output of FreeSurfer e.g the lh.aparc.annot into an ".nii" so i can see the parcels in Mricro. Now I can see the parcels just on the cortex not on the whole graymatter. The first question I have is that, is the parcellation done on the whole graymatter? And if yes, is there a way that I can see the volumes on the whole graymatter, not just on the cortex? I would be grateful if you could help me. best regards, Maedeh,___ 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] A Help Request for Random Parcellation
External Email - Use Caution Dear Dr.Bruce Fischle; Thank you very much for all help you have given me so far,I would like to know if it is possible to access the algorithms(or any specific parts of them) that run FreeSurfer and I also would like to know if I can do a random parcellation by FreeSurfer. Thanks in advance. Kind regards; Maedeh;___ 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] "A question about mris_divide_parcellation"
External Email - Use Caution Dear Dr.Bruce Fischl Thx for replying. You told me that inequality of the subregions depends on the code I ran. First off I ran the command: recon-all -subject test -i data_00.nii -all "data_00.nii" is a raw MR image. Then, I ran this command: mris_divide_parcellation test lh aparc.annot splitfile.txt lh.aparc.split And splitfile is a 2-column file I myself made based on the FreeSurFerColorLUT.txt's content according to the description in "mris_divide_parcellation --help". And that's it I would be grateful if you could help me. Kind regards;___ 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] A Question about mris_divide_parcellation
External Email - Use Caution Dear experts; By using "recon-all", I have parcellated an MR image and by using "mris_divide_parcellation" i have subdivided the result into specific regions,(each region has been divided into 10 subregions), the question I have is that are these subregions equal sized? Are they equal sized within the whole cortex or within each region? In other words,if i have 340 regions par hemisphere,are they all equal sized or not? How can check and get it?___ 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] The Problem Using "mris_ca_train"
External Email - Use Caution Dear FreeSurfer experts, I would like to use the FreeSurfer package to do a parcellation.Just for testing, I am using "buckner_data" and there is a step I have been stuck in.I have problem using "mris_ca_train" command.This is the whole code I run on my terminal to create my own atlas: [user@localhost ~]$ export FREESURFER_HOME=/usr/local/freesurfer [user@localhost ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni [user@localhost ~]$ export TUTORIAL_DATA=/home/user/Desktop/ramezani/tutorial/ [user@localhost ~]$ export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs [user@localhost ~]$ cd $SUBJECTS_DIR [user@localhost tutorial_subjs]$ mris_ca_train -n2 rh rh.sphere.reg rh.aparc.annot good_output ./rh.my_atlas.gcs Usage: -- mris_ca_train [options] ... [user@localhost tutorial_subjs]$ As you see it just goes to the next line and doesn't show any errors so I can get where the problem is from. That would be great if you could help me. Best regards;Maedeh___ 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] (no subject)
External Email - Use Caution Dear FreeSurfer experts, I would like to use the FreeSurfer package to do a parcellation.Just for testing, I am using "buckner_data" and there is a step I have been stuck in.I have problem using "mris_ca_train" command.This is the whole code I run on my terminal to create my own atlas: [user@localhost ~]$ export FREESURFER_HOME=/usr/local/freesurfer [user@localhost ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni [user@localhost ~]$ export TUTORIAL_DATA=/home/user/Desktop/ramezani/tutorial/ [user@localhost ~]$ export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs [user@localhost ~]$ cd $SUBJECTS_DIR [user@localhost tutorial_subjs]$ mris_ca_train -n2 rh rh.sphere.reg rh.aparc.annot good_output ./rh.my_atlas.gcs Usage: -- mris_ca_train [options] ... [user@localhost tutorial_subjs]$ As you see it just goes to the next line and doesn't show any errors so I can get where the problem is from. That would be great if you could help me. Best regards;Maedeh___ 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] A Help Request for Freesurfer Installing
External Email - Use Caution Hello; This is Maedeh Khalilian, a master student at Shiraz University of Technology. I have ubuntu 18.04 LTS installed on my laptop. I have already installed Freesurfer package but it is the version for CentOS. I wonder if I can use it with ubuntu. I would appreciate if you could help me. Best regards;___ 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.
