Re: [Freesurfer] Working with MEMPRAGE
Hi Jonathan, FreeSurfer folks: Did you have success in combining 4 echoes of MEMPRAGE images into one? I went through the archives and it appears to me that you would use: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh only after the scan has been through the recon all process. My question is did you use mri-concat to combine the 4 echoes into one? thanks, Alan On Mon, May 13, 2013 at 11:26 AM, Jonathan Holt whats...@umich.edu wrote: Bruce, how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: Hi all, last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: tkmedit subjid brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: Hi all, I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! Thanks, -Kayle From: Douglas Greve gr...@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.eduwrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote
Re: [Freesurfer] Working with MEMPRAGE
Hi Alan to use the 4 echoes you want to compute the rms. I think something like mri_average -noconform -sqr mprage_echo?.mgz mprage_rms.mgz should do the trick (then use mprage_rms.mgz as the input to recon-all) cheers Bruce On Mon, 15 Jul 2013, Alan Francis wrote: Hi Jonathan, FreeSurfer folks: Did you have success in combining 4 echoes of MEMPRAGE images into one? I went through the archives and it appears to me that you would use: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh only after the scan has been through the recon all process. My question is did you use mri-concat to combine the 4 echoes into one? thanks, Alan On Mon, May 13, 2013 at 11:26 AM, Jonathan Holt whats...@umich.edu wrote: Bruce, how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: Hi all, last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: tkmedit subjid brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: Hi all, I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! Thanks, -Kayle From: Douglas Greve gr...@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis
Re: [Freesurfer] Working with MEMPRAGE
Thanks Bruce. On Mon, Jul 15, 2013 at 4:52 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Alan to use the 4 echoes you want to compute the rms. I think something like mri_average -noconform -sqr mprage_echo?.mgz mprage_rms.mgz should do the trick (then use mprage_rms.mgz as the input to recon-all) cheers Bruce On Mon, 15 Jul 2013, Alan Francis wrote: Hi Jonathan, FreeSurfer folks: Did you have success in combining 4 echoes of MEMPRAGE images into one? I went through the archives and it appears to me that you would use: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh only after the scan has been through the recon all process. My question is did you use mri-concat to combine the 4 echoes into one? thanks, Alan On Mon, May 13, 2013 at 11:26 AM, Jonathan Holt whats...@umich.edu wrote: Bruce, how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: Hi all, last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: tkmedit subjid brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.**mgz -surface $SUBJECTS_DIR/subjid/surf/lh.**white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.**white -aparc+aseg this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: Hi all, I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_**64-stable-v5.3.0-BETA-**20130509. On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_**edits/OB01_orig/ /space/ficus/6/users/SNEF_**edits/OB01_orig_dura/ I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! Thanks, -Kayle From: Douglas Greve gr...@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz
Re: [Freesurfer] Working with MEMPRAGE
Hi all, last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: tkmedit subjid brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: Hi all, I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! Thanks, -Kayle From: Douglas Greve gr...@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work
Re: [Freesurfer] Working with MEMPRAGE
Hi Jon there shouldn't be more surfaces I don't think - the ?h.white and ?h.pial should still be the ones you look at Bruce On Mon, 13 May 2013, Jonathan Holt wrote: Hi all, last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: tkmedit subjid brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: Hi all, I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! Thanks, -Kayle From: Douglas Greve gr...@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required
Re: [Freesurfer] Working with MEMPRAGE
Bruce, how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: Hi all, last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: tkmedit subjid brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: Hi all, I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! Thanks, -Kayle From: Douglas Greve gr...@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50
Re: [Freesurfer] Working with MEMPRAGE
you can use file-aux-surfaces-load aux main surface (or something like that). Or use freeview. cheers Bruce On Mon, 13 May 2013, Jonathan Holt wrote: Bruce, how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: Hi all, last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: tkmedit subjid brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: Hi all, I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! Thanks, -Kayle From: Douglas Greve gr...@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different
Re: [Freesurfer] Working with MEMPRAGE
p.s. make sure that the echoes are in float format, not uchar/int/short (you need to use -odt float in the mri_convert command line) On Mon, 13 May 2013, Bruce Fischl wrote: you can use file-aux-surfaces-load aux main surface (or something like that). Or use freeview. cheers Bruce On Mon, 13 May 2013, Jonathan Holt wrote: Bruce, how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: Hi all, last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: tkmedit subjid brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: Hi all, I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! Thanks, -Kayle From: Douglas Greve gr...@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh
Re: [Freesurfer] Working with MEMPRAGE
I'll definitely do that next time... although it didn't seem to pose any noticeable issues this time around? jon On May 13, 2013, at 3:52 PM, Bruce Fischl wrote: p.s. make sure that the echoes are in float format, not uchar/int/short (you need to use -odt float in the mri_convert command line) On Mon, 13 May 2013, Bruce Fischl wrote: you can use file-aux-surfaces-load aux main surface (or something like that). Or use freeview. cheers Bruce On Mon, 13 May 2013, Jonathan Holt wrote: Bruce, how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: Hi all, last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: tkmedit subjid brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: Hi all, I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! Thanks, -Kayle From: Douglas Greve gr...@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl
Re: [Freesurfer] Working with MEMPRAGE
I'm surprised it would work well if they are not float. You'll lose a lot of precision On Mon, 13 May 2013, Jonathan Holt wrote: I'll definitely do that next time... although it didn't seem to pose any noticeable issues this time around? jon On May 13, 2013, at 3:52 PM, Bruce Fischl wrote: p.s. make sure that the echoes are in float format, not uchar/int/short (you need to use -odt float in the mri_convert command line) On Mon, 13 May 2013, Bruce Fischl wrote: you can use file-aux-surfaces-load aux main surface (or something like that). Or use freeview. cheers Bruce On Mon, 13 May 2013, Jonathan Holt wrote: Bruce, how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: Hi all, last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: tkmedit subjid brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: Hi all, I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! Thanks, -Kayle From: Douglas Greve gr...@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all
Re: [Freesurfer] Working with MEMPRAGE
I wont question it, but this is my first multi echo brain and it's the most beautiful i've ever seen. so crisp. On May 13, 2013, at 3:55 PM, Bruce Fischl wrote: I'm surprised it would work well if they are not float. You'll lose a lot of precision On Mon, 13 May 2013, Jonathan Holt wrote: I'll definitely do that next time... although it didn't seem to pose any noticeable issues this time around? jon On May 13, 2013, at 3:52 PM, Bruce Fischl wrote: p.s. make sure that the echoes are in float format, not uchar/int/short (you need to use -odt float in the mri_convert command line) On Mon, 13 May 2013, Bruce Fischl wrote: you can use file-aux-surfaces-load aux main surface (or something like that). Or use freeview. cheers Bruce On Mon, 13 May 2013, Jonathan Holt wrote: Bruce, how is it that I might load multiple surfaces, loading lh after having loaded rh makes the other disappear. this is loading manually, not from the command line On May 13, 2013, at 11:14 AM, Jonathan Holt wrote: Hi all, last question promise. Successfully completed mris_make_surfaces for both hemispheres. in my day-to-day editing I open tkmedit thusly: tkmedit subjid brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface $SUBJECTS_DIR/subjid/surf/lh.white -aux-surface $SUBJECTS_DIR/subjid/surf/rh.white -aparc+aseg this works for mprage subjects. In evaluating and possibly editing MEMPRAGE subjects, which surfaces should I have opened in tkmedit, as there seem to be many more this time around. best, jon On May 11, 2013, at 6:49 PM, Bruce Fischl wrote: Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: Hi all, I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! Thanks, -Kayle From: Douglas Greve gr...@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns
Re: [Freesurfer] Working with MEMPRAGE
Hi Kayle it's been a long time since I wrote that code and we've only run it a few times. If you upload your subject directory I'll take a look cheers Bruce On Sat, 11 May 2013, Kayle Sawyer wrote: Hi all, I tried to use the 4-echo MEMPRAGE dura detection for mris_make_surfaces, but I'm not sure if it worked. The terminal output, including commands, is attached. It was run with version freesurfer-Linux-centos6_x86_64-stable-v5.3.0-BETA-20130509. On the original recon, in the rh, there is a segment of dura marked as grey inside the pial line, at 94 111 169. The surfaces did not appear to change substantially after I reran mris_make_surfaces with the -dura flag specifying the 4-echo MEMPRAGE, which I placed in the mri directory. You can see the before and after for yourself on the attached screenshots, or if you have NMR access, here: /space/ficus/6/users/SNEF_edits/OB01_orig/ /space/ficus/6/users/SNEF_edits/OB01_orig_dura/ I saw this output from mris_make_surfaces for the rh, so maybe -dura did correct a different defect? 7 non-cortical segments detected only using segment with 1900 vertices Any help would be appreciated, because we have over 130 brains and the fewer manual corrections, the better! Thanks, -Kayle From: Douglas Greve gr...@nmr.mgh.harvard.edu Date: Thu, May 9, 2013 at 8:44 PM Subject: Re: [Freesurfer] Working with MEMPRAGE To: freesurfer@nmr.mgh.harvard.edu the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon ___ 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
Re: [Freesurfer] Working with MEMPRAGE
I've gotten as far as running the mris_make_surfaces on the RMS, but after running for a bit it stopped with this error mghRead (file/path/s_MEMPRAGE/mri/0010.mgz -1): coult not open file mris_make_surfaces: could not read 0th echo for dura localization from file/path/s_MEMPRAGE/mri/0010.mgz for reference, the RMS file name is 001.mgz jon On May 9, 2013, at 8:44 PM, Douglas Greve wrote: the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Working with MEMPRAGE
can you send details about the steps you carried out including full command lines? On Fri, 10 May 2013, Jonathan Holt wrote: I've gotten as far as running the mris_make_surfaces on the RMS, but after running for a bit it stopped with this error mghRead (file/path/s_MEMPRAGE/mri/0010.mgz -1): coult not open file mris_make_surfaces: could not read 0th echo for dura localization from file/path/s_MEMPRAGE/mri/0010.mgz for reference, the RMS file name is 001.mgz jon On May 9, 2013, at 8:44 PM, Douglas Greve wrote: the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon ___ 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 ___ 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
Re: [Freesurfer] Working with MEMPRAGE
$ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer $ mris_make_surfaces -dura 001%d.mgz 4 s_MEMPRAGE lh it's entirely possible I'm specifying the wrong mgz? After running recon-all on the RMS the usual directories were created, etc... including 001.mgz which is in s_MEMPRAGE/mri/orig. On Fri, May 10, 2013 at 12:39 PM, Jonathan Holt whats...@umich.edu wrote: $ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer $ mris_make_surfaces -dura 001%d.mgz 4 s_MEMPRAGE lh it's entirely possible I'm specifying the wrong mgz? After running recon-all on the RMS the usual directories were created, etc... including 001.mgz which is in s_MEMPRAGE/mri/orig. On Fri, May 10, 2013 at 12:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: can you send details about the steps you carried out including full command lines? On Fri, 10 May 2013, Jonathan Holt wrote: I've gotten as far as running the mris_make_surfaces on the RMS, but after running for a bit it stopped with this error mghRead (file/path/s_MEMPRAGE/mri/**0010.mgz -1): coult not open file mris_make_surfaces: could not read 0th echo for dura localization from file/path/s_MEMPRAGE/mri/0010.**mgz for reference, the RMS file name is 001.mgz jon On May 9, 2013, at 8:44 PM, Douglas Greve wrote: the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.**harvard.edufreesurfer-requ...@nmr.mgh.harvard.eduwrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.02.**1305091043500.13...@gate.nmr.** mgh.harvard.edualpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __**_ Freesurfer mailing list
Re: [Freesurfer] Working with MEMPRAGE
-0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce
Re: [Freesurfer] Working with MEMPRAGE
Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9
Re: [Freesurfer] Working with MEMPRAGE
9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject
Re: [Freesurfer] Working with MEMPRAGE
, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May
Re: [Freesurfer] Working with MEMPRAGE
, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory
Re: [Freesurfer] Working with MEMPRAGE
Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon ___ 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] Working with MEMPRAGE
Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Working with MEMPRAGE
can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon 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] Working with MEMPRAGE
I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon 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] Working with MEMPRAGE
it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon 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] Working with MEMPRAGE
That was my suspicion, I've got them in the wrong folder. None of them are 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and nothing else. Also the exact error has it looking in /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz as opposed to /example/directory/subjects/subjid/mri/filled.mgz I can rename subject directory if need be. On May 9, 2013, at 10:54 AM, Bruce Fischl wrote: is your SUBJECTS_DIR set properly? You need to put the memprage echoes in the subject's mri dir On Thu, 9 May 2013, Jonathan Holt wrote: Oh, simple mistake! However, now it spit's an error saying I need filled.mgz? On May 9, 2013, at 10:44 AM, Bruce Fischl wrote: it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon 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 ___ 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] Working with MEMPRAGE
Did you run recon-all? It will create filled.mgz in the subject/mri dir On May 9, 2013, at 11:00 AM, Jonathan Holt whats...@umich.edu wrote: That was my suspicion, I've got them in the wrong folder. None of them are 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and nothing else. Also the exact error has it looking in /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz as opposed to /example/directory/subjects/subjid/mri/filled.mgz I can rename subject directory if need be. On May 9, 2013, at 10:54 AM, Bruce Fischl wrote: is your SUBJECTS_DIR set properly? You need to put the memprage echoes in the subject's mri dir On Thu, 9 May 2013, Jonathan Holt wrote: Oh, simple mistake! However, now it spit's an error saying I need filled.mgz? On May 9, 2013, at 10:44 AM, Bruce Fischl wrote: it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon 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 ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Working with MEMPRAGE
No, I believe my PI simply ran mri_convert on the 4 nii's, Clearly there is a better approach? jon On May 9, 2013, at 11:04 AM, Bruce Fischl wrote: Did you run recon-all? It will create filled.mgz in the subject/mri dir On May 9, 2013, at 11:00 AM, Jonathan Holt whats...@umich.edu wrote: That was my suspicion, I've got them in the wrong folder. None of them are 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and nothing else. Also the exact error has it looking in /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz as opposed to /example/directory/subjects/subjid/mri/filled.mgz I can rename subject directory if need be. On May 9, 2013, at 10:54 AM, Bruce Fischl wrote: is your SUBJECTS_DIR set properly? You need to put the memprage echoes in the subject's mri dir On Thu, 9 May 2013, Jonathan Holt wrote: Oh, simple mistake! However, now it spit's an error saying I need filled.mgz? On May 9, 2013, at 10:44 AM, Bruce Fischl wrote: it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon 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 ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Working with MEMPRAGE
Hi Jon you need to run recon-all all the way through, then run the command I sent you with the echoes in the mri dir cheers Bruce On Thu, 9 May 2013, Jonathan Holt wrote: No, I believe my PI simply ran mri_convert on the 4 nii's, Clearly there is a better approach? jon On May 9, 2013, at 11:04 AM, Bruce Fischl wrote: Did you run recon-all? It will create filled.mgz in the subject/mri dir On May 9, 2013, at 11:00 AM, Jonathan Holt whats...@umich.edu wrote: That was my suspicion, I've got them in the wrong folder. None of them are 'filled.mgz' though, I've only got 4 echoes (memprage_echo 1-4 .mgz) and nothing else. Also the exact error has it looking in /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz as opposed to /example/directory/subjects/subjid/mri/filled.mgz I can rename subject directory if need be. On May 9, 2013, at 10:54 AM, Bruce Fischl wrote: is your SUBJECTS_DIR set properly? You need to put the memprage echoes in the subject's mri dir On Thu, 9 May 2013, Jonathan Holt wrote: Oh, simple mistake! However, now it spit's an error saying I need filled.mgz? On May 9, 2013, at 10:44 AM, Bruce Fischl wrote: it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon 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 ___ 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 ___ 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] Working with MEMPRAGE
Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon ___ 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] Working with MEMPRAGE
Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon ___ 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] Working with MEMPRAGE
the dcmunpack command is right. You should make sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: -run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Working with MEMPRAGE To: Jonathan Holt whats...@umich.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.02.1305091043500.13...@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII it needs to be: mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh note the 4 which tells it how many echoes to read On Thu, 9 May 2013, Jonathan Holt wrote: I input: mris_make_surfaces -dura memprage_echo%d.mgz subjid lh it returns: detecting dura using 0 echos from memprage_echo%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command line? It should say 4 echoes, not 0 On Thu, 9 May 2013, Jonathan Holt wrote: Thanks Bruce, should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? Also, should the fact that after running mris_make_surfaces, it says detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon ___ 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 ___ 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] Working with MEMPRAGE
Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands is the appropriate mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? jon ___ 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.
