[Freesurfer] Cortical Thickness
Hello Freesurfer Experts, I finished running the qdec analysis on our patient and healthy control populations. While looking at the clusters I am having a hard time telling which group -controls or patients have a larger cortical thickness? Additionally, I wanted to know if it would be possible to save the images created by qdec as a jpeg or png file. I would greatly appreciate your help. Thanks, Gaurang ___ 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] QDEC-Cortical Thickness
Hello Freesurfer Experts, I want to compare the cortical thickness between the groups (HC & Patients), and wanted to know where qdec shows this information. Once the design tab is loaded, I am seeing the question in the analysis results – does the correlation between thickness and Age differ from zero? Do I need to a run the command for GLM in order to see if there is a cortical difference between the two populations? I would greatly appreciate your help. Thanks, Gaurang ___ 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] subject directory
This is the output and the subsequent error I receive. How do I run this command (from the tutorial- I already ran –qcached recon-all on my data) mris_preproc --fsgd gender_age.fsgd \ > --cache-in thickness.fwhm10.fsaverage \ > --target fsaverage \ > --hemi lh \ > --out lh.gender_age.thickness.10.mgh nsubjects = 103 ERROR: cannot find /home/limachi/freesurfer/subjects/CON_202/surf/lh.thickness.fwhm10.fsaverage.mgh Thanks, Gaurang From: Douglas Greve <gr...@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Sunday, March 12, 2017 at 6:56 PM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subject directory Can you send the entire terminal output (not just the error) On 3/10/17 4:01 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote: The error is ERROR: cannot find /home/username/freesurfer/subjects/surf/lh.thickness.fwhm10.fsaverage.mgh However, the file should run on /servername/username/FATCAT/subjects/… I don’t know why it tries to find the files in the default home/… folders. Thanks, Gaurang From: Douglas Greve <gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, March 9, 2017 at 10:45 PM To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subject directory can you send the terminal entire output that includes the error? On 3/9/17 7:57 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote: Dear Freesurfer Experts, I want to customize the directory so I can run the following command mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh However, after running this command it keeps checking in the wrong directory for the files. How do I change the directory, do I change it in the FSGD file I made or somewhere else? I ran the recon-all qcache, but I need to run this on the previously cached data. I would greatly appreciate it if you can assist me with this problem. Best Regards, Gaurang Shyam LImachia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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] subject directory
The error is ERROR: cannot find /home/username/freesurfer/subjects/surf/lh.thickness.fwhm10.fsaverage.mgh However, the file should run on /servername/username/FATCAT/subjects/… I don’t know why it tries to find the files in the default home/… folders. Thanks, Gaurang From: Douglas Greve <gr...@nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Thursday, March 9, 2017 at 10:45 PM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] subject directory can you send the terminal entire output that includes the error? On 3/9/17 7:57 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote: Dear Freesurfer Experts, I want to customize the directory so I can run the following command mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh However, after running this command it keeps checking in the wrong directory for the files. How do I change the directory, do I change it in the FSGD file I made or somewhere else? I ran the recon-all qcache, but I need to run this on the previously cached data. I would greatly appreciate it if you can assist me with this problem. Best Regards, Gaurang Shyam LImachia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] subject directory
Dear Freesurfer Experts, I want to customize the directory so I can run the following command mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh However, after running this command it keeps checking in the wrong directory for the files. How do I change the directory, do I change it in the FSGD file I made or somewhere else? I ran the recon-all qcache, but I need to run this on the previously cached data. I would greatly appreciate it if you can assist me with this problem. Best Regards, Gaurang Shyam LImachia ___ 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] GLM-error
Dear Freesurfer Experts, I was running qdec, and encountered an error while I was running the analyze button on the qdec. Subsequently, if you can help with the following error would greatly appreciate it. Continuous Variable Means (all subjects) 0 Intracranial_volume 1.53095e+06 157812 1 Gender 1.75728 0.428726 Class Means of each Continuous Variable 1 Main 1530945.8883 1.7573 INFO: gd2mtx_method is dods Reading source surface /raids/hmcsraid3/silvina/PMD_FATCAT2015/fsaverage/surf/lh.white MRISread(/raids/hmcsraid3/silvina/PMD_FATCAT2015/fsaverage/surf/lh.white): could not open file No such file or directory mri_glmfit: could not read surface /raids/hmcsraid3/silvina/PMD_FATCAT2015/fsaverage/surf/lh.white No such file or directory Error in Analyze: command failed: mri_glmfit --y /raids/hmcsraid3/silvina/PMD_FATCAT2015/qdec/Untitled/y.mgh --fsgd /raids/hmcsraid3/silvina/PMD_FATCAT2015/qdec/Untitled/qdec.fsgd dods --glmdir /raids/hmcsraid3/silvina/PMD_FATCAT2015/qdec/Untitled --surf fsaverage lh --C /raids/hmcsraid3/silvina/PMD_FATCAT2015/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /raids/hmcsraid3/silvina/PMD_FATCAT2015/qdec/Untitled/contrasts/lh-Avg-thickness-Intracranial_volume-Cor.mat Thanks, Gaurang Shyam Limachia ___ 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
Hello Freesurfer Experts, I received this error while running the make_avg_subject script. I would greatly appreciate it if you can point me in the right direction. Also, I do not know how the aparc.annot file is supposed to be created. not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization... processing subject CON_201 (1 of 98) reading spherical surface /raids/hmcsraid3/silvina/PMD_FATCAT2015/CON_201/surf/lh.sphere.reg... could not read annot file /raids/hmcsraid3/silvina/PMD_FATCAT2015/CON_201/surf/../label/lh.aparc.annot No such file or directory mris_make_template: could not read annot file aparc No such file or directory ERROR: make_average_surface Thanks, Gaurang Shyam Limachia ___ 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
Dear Freesurfer Experts, I received this error while running the make_avg_subject script. I would greatly appreciate it if you can point me in the right direction. Also, I do not know how the aparc.annot file is supposed to be created. not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization... processing subject CON_201 (1 of 98) reading spherical surface /raids/hmcsraid3/silvina/PMD_FATCAT2015/CON_201/surf/lh.sphere.reg... could not read annot file /raids/hmcsraid3/silvina/PMD_FATCAT2015/CON_201/surf/../label/lh.aparc.annot No such file or directory mris_make_template: could not read annot file aparc No such file or directory ERROR: make_average_surface Thanks, Gaurang Shyam Limachia ___ 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] Qdec Error
Dear Fressurfer Experts, My table.dat file loaded fine. However, I came across the following error when I was running the Qdec generate stats data table. If you can let me know what I can do to fix the following error I would greatly appreciate it. Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /local/limachiagv/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects CON_201 CON_202 CON_203 CON_204 CON_205 CON_206 CON_207 CON_209 CON_211 CON_212 CON_213 CON_214 CON_215 CON_216 CON_217 CON_218 CON_219 CON_220 CON_221 CON_222 CON_223 CON_225 CON_226 CON_227 CON_228 CON_230 CON_231 CON_232 CON_233 CON_234 CON_235 CON_236 CON_237 CON_239 CON_240 CON_241 CON_242 CON_244 CON_245 CON_246 CON_247 CON_248 CON_249 CON_250 CON_251 CON_252 CON_253 CON_254 CON_255 CON_256 CON_257 CON_258 CON_259 CON_260 PAT_402 PAT_403 PAT_407 PAT_409 PAT_410 PAT_411 PAT_412 PAT_413 PAT_414 PAT_415 PAT_416 PAT_417 PAT_418 PAT_419 PAT_421 PAT_422 PAT_424 PAT_425 PAT_426 PAT_427 PAT_428 PAT_429 PAT_430 PAT_431 PAT_432 PAT_433 PAT_437 PAT_439 PAT_440 SUBJECTS_DIR : /local/limachiagv/freesurfer/subjects Parsing the .stats files ERROR: The stats file /local/limachiagv/freesurfer/subjects/CON_201/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thanks, Gaurang ___ 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] Qdec Generate Stats Data Table Error
Hello All, My table.dat file loaded fine. However, I came across the following error when I was running the Qdec generate stats data table. If you can let me know what I can do to fix the following error I would greatly appreciate it. Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /local/limachiagv/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects CON_201 CON_202 CON_203 CON_204 CON_205 CON_206 CON_207 CON_209 CON_211 CON_212 CON_213 CON_214 CON_215 CON_216 CON_217 CON_218 CON_219 CON_220 CON_221 CON_222 CON_223 CON_225 CON_226 CON_227 CON_228 CON_230 CON_231 CON_232 CON_233 CON_234 CON_235 CON_236 CON_237 CON_239 CON_240 CON_241 CON_242 CON_244 CON_245 CON_246 CON_247 CON_248 CON_249 CON_250 CON_251 CON_252 CON_253 CON_254 CON_255 CON_256 CON_257 CON_258 CON_259 CON_260 PAT_402 PAT_403 PAT_407 PAT_409 PAT_410 PAT_411 PAT_412 PAT_413 PAT_414 PAT_415 PAT_416 PAT_417 PAT_418 PAT_419 PAT_421 PAT_422 PAT_424 PAT_425 PAT_426 PAT_427 PAT_428 PAT_429 PAT_430 PAT_431 PAT_432 PAT_433 PAT_437 PAT_439 PAT_440 SUBJECTS_DIR : /local/limachiagv/freesurfer/subjects Parsing the .stats files ERROR: The stats file /local/limachiagv/freesurfer/subjects/CON_201/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Thanks, Gaurang ___ 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] Hippocampus & Amygdala Volume Accuracy
Hello Bruce, I am uploading the data set to filedrop for you to look over. Can you assist us in determining the optimal method for parcellation of the white and gray matter. We are particularly interested in determining the volume of the hippocampus and amygdala. Are there any special parameters we should use for these structures? Therefore, we want to improve the accuracy of the pial and white matter surfaces. I would greatly appreciate your help. Best Regards, Shyam ___ 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] converting ME-MPRAGE files
We ran the following command, but the clarity improved minimally. Therefore, is there another command that you would recommend. Thanks, Gaurang On 6/9/16, 5:30 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: >That tells you there is one "series" in that folder. The series here >means a volume, though there are many dicom files. >dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm is just one in the series. >To use this, you can run > >recon-all -s yoursubject -all -i >dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm > >or > >mri_convert dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm output.nii.gz > > > > > >On 06/09/2016 05:11 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote: >> Hello All, >> >> We have acquired our anatomical images on a Siemens scanner as >> multiecho MPRAGE sequence (4 echos), and wish to unpack the runs so we >> can perform morphometric analysis using FreeSurfer. What is the >> optimal way to convert the DICOM files so we can use them with >> FreeSurfer tools? Specifically, what command line do you recommend for >> dcmunpack? >> >> When running the command: dcmunpack src dicomdir we get the >> following output: >> Found 1 unique series: 6 >> 6 3D_T1_MEMPRAGE 7.27 2530 7 unknown ROW 650 >> dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm >> Not sure how to interpret this. >> >> Thanks. >> >> Gaurang Limachia >> >> >> ___ >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >___ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom it >is >addressed. If you believe this e-mail was sent to you in error and the >e-mail >contains patient information, please contact the Partners Compliance >HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in >error >but does not contain patient information, please contact the sender and >properly >dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] converting ME-MPRAGE files
Hello All, We have acquired our anatomical images on a Siemens scanner as multiecho MPRAGE sequence (4 echos), and wish to unpack the runs so we can perform morphometric analysis using FreeSurfer. What is the optimal way to convert the DICOM files so we can use them with FreeSurfer tools? Specifically, what command line do you recommend for dcmunpack? When running the command: dcmunpack –src dicomdir we get the following output: Found 1 unique series: 6 6 3D_T1_MEMPRAGE 7.27 2530 7 unknown ROW 650 dicomdir/mr_0006-e02/3d_t1_memprage-00533.dcm Not sure how to interpret this. Thanks. Gaurang Limachia ___ 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] WM & GM Parcellation Edit
Yes the green circles are control points. The control points shown in the picture show surfaces we feel are not accurate. Additionally, how are we supposed to use the control points, do we place them on the inner most boundary of the WM? Also, going back to the original questions: How do you recommend that we proceed to obtain the most accurate results? Should we continue making changes to the wm.mgz file as well as adding control points, or is it sufficient just to add control points? Thanks, Shyam On 5/31/16, 3:33 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Shyam > >can you add arrows to show where you don't think the surfaces are >accurate? > >And are the green circles meant to be control points? If so, I'm >surprised that didn't break everything since they need to be added to the >interior of the WM. > >cheers >Bruce > > >On Tue, 31 May 2016, Limachia, >Gaurang (NIH/NINDS) [F] wrote: > >> Hi freesurfer community, >> >> We are checking to see the accuracy of our subjects¹ white and gray >>matter >> parcellation. We have found that for some subjects the contour lines for >> white matter surface and pial surface are somewhat inaccurate, and have >>been >> making modifications using the tutorials. >> >> Specifically, we made changes to the white matter wm.mgz file; this >>however >> did not alter the contour lines. We also used control points, and were >>able >> to see changes to the white matter surface contour lines using this >> approach. >> >> How do you recommend that we proceed to obtain the most accurate >>results? >> Should we continue making changes to the wm.mgz file as well as adding >> control points, or is it sufficient just to add control points? >> >> I am attaching a screen shot which shows changes to the contour lines >>after >> we added control points. >> >> Best Regards, >> >> Shyam [IMAGE][IMAGE] >> ___ 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
The way I made the changes was that I followed the following tutorial exactly to make the changes to the white matter. If there is a another way not shown in the tutorial, can you please let me know. I would greatly appreciate it. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_free v iew Thanks, Gaurang Shyam On 5/18/16, 10:02 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >sorry, I still don't understand. Which file are you adding white matter >to? From the image you sent it looks like you are drawing on the brain or >one of the similar ones, which is not what you should be doing. You >should >load and edit the wm.mgz > >cheers >Bruce > > >On Tue, 17 May 2016, Limachia, Gaurang (NIH/NINDS) [F] wrote: > >> I made the necessary changes to the white matter, and when I ran recon >>all >> the changes with the voxels showed up, but there was no change to the >> contour lines. In order to change the gray matter volume, I can¹t find >>the >> changes I already made on the white matter (the picture with green >>control >> points). If I am able to see the changes I made to the white matter, I >>can >> utilize the control points to modify the segmentation. Also will this >> impact the gray matter volume as well as per your previous response to >>my >> question. >> >> Thanks, >> >> Gaurang >> ___ 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
So I followed the following tutorial exactly to make the changes to the white matter. If there is a another way not shown in the tutorial, can you please let me know. I would greatly appreciate it. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freev iew Thanks, Gaurang Shyam On 5/18/16, 10:02 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >sorry, I still don't understand. Which file are you adding white matter >to? From the image you sent it looks like you are drawing on the brain or >one of the similar ones, which is not what you should be doing. You >should >load and edit the wm.mgz > >cheers >Bruce > > >On Tue, 17 May 2016, Limachia, Gaurang (NIH/NINDS) [F] wrote: > >> I made the necessary changes to the white matter, and when I ran recon >>all >> the changes with the voxels showed up, but there was no change to the >> contour lines. In order to change the gray matter volume, I can¹t find >>the >> changes I already made on the white matter (the picture with green >>control >> points). If I am able to see the changes I made to the white matter, I >>can >> utilize the control points to modify the segmentation. Also will this >> impact the gray matter volume as well as per your previous response to >>my >> question. >> >> Thanks, >> >> Gaurang >> ___ 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 (white/grey matter changes)
Dr. Fischl, I loaded the t1 file from our patient dataset freesurfer>t1>mri>wm.mgz. When I was editing the white matter, I had the wm highlighted, and not brainmask under the volumes. Best, Gaurang On 5/17/16, 5:56 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Gaurang > >it looks like you edited the white matter, but not in the wm.mgz, which >is what we require. What volume (i.e. what was the name of the file you >loaded) did you edit? > >cheers >Bruce >On Tue, 17 May 2016, Limachia, Gaurang (NIH/NINDS) [F] >wrote: > >> I edited the white matter, and then ran recon-all command. The image I >> included shows that the white matter changes, but the contour lines have >> not changed. Subsequently, how do I change the contour lines to reflect >> the changes I made to the white matter. Additionally, is changing the >> control points the way to change grey matter? >> >> Thanks, >> >> Gaurang >> >> On 5/17/16, 5:44 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >>> Hi Gaurang >>> >>> what volume are you editing? You should be editing the wm.mgz. >>> >>> cheers >>> Bruce >>> >>> On Tue, 17 >>> May 2016, Limachia, Gaurang (NIH/NINDS) [F] wrote: >>> >>>> This is how the white matter changes look like after making >>>>corrections >>>> and >>>> running recon all. >>>> >>>> From: "Limachia , Gaurang (NIH/NINDS) [F]" <gaurang.limac...@nih.gov> >>>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>>> Date: Tuesday, May 17, 2016 at 4:49 PM >>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>>> Subject: [Freesurfer] Freesurfer >>>> >>>> I made the necessary changes to the white matter, and when I ran recon >>>> all >>>> the changes with the voxels showed up, but there was no change to the >>>> contour lines. In order to change the gray matter volume, I can¹t find >>>> the >>>> changes I already made on the white matter (the picture with green >>>> control >>>> points). If I am able to see the changes I made to the white matter, I >>>> can >>>> utilize the control points to modify the segmentation. Also will this >>>> impact the gray matter volume as well as per your previous response to >>>> my >>>> question. >>>> >>>> Thanks, >>>> >>>> Gaurang >>>> >> >> >> ___ >> 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] Freesurfer (white/grey matter changes)
I edited the white matter, and then ran recon-all command. The image I included shows that the white matter changes, but the contour lines have not changed. Subsequently, how do I change the contour lines to reflect the changes I made to the white matter. Additionally, is changing the control points the way to change grey matter? Thanks, Gaurang On 5/17/16, 5:44 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Gaurang > >what volume are you editing? You should be editing the wm.mgz. > >cheers >Bruce > >On Tue, 17 >May 2016, Limachia, Gaurang (NIH/NINDS) [F] wrote: > >> This is how the white matter changes look like after making corrections >>and >> running recon all. >> >> From: "Limachia , Gaurang (NIH/NINDS) [F]" <gaurang.limac...@nih.gov> >> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Date: Tuesday, May 17, 2016 at 4:49 PM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: [Freesurfer] Freesurfer >> >> I made the necessary changes to the white matter, and when I ran recon >>all >> the changes with the voxels showed up, but there was no change to the >> contour lines. In order to change the gray matter volume, I can¹t find >>the >> changes I already made on the white matter (the picture with green >>control >> points). If I am able to see the changes I made to the white matter, I >>can >> utilize the control points to modify the segmentation. Also will this >> impact the gray matter volume as well as per your previous response to >>my >> question. >> >> Thanks, >> >> Gaurang >> ___ 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.
