[Freesurfer] Error: cannot determine file type
Hi all, Am receiving the below error, I haven't used this scan before but have never had issues with .dcm. Sorry I'm not sure what sort of scanner they are from. Any help would be appreciated. Cheers, Will /usr/local/freesurfer/subjects/YU mri_convert /home/will/Dropbox/BrainformLtd/Freesurfer/October2015/YU/YUScan1/1.3.12.2.1107.5.2.36.40463.20130122101900878319572.dcm /usr/local/freesurfer/subjects/YU/mri/orig/001.mgz mri_convert /home/will/Dropbox/BrainformLtd/Freesurfer/October2015/YU/YUScan1/1.3.12.2.1107.5.2.36.40463.20130122101900878319572.dcm /usr/local/freesurfer/subjects/YU/mri/orig/001.mgz ERROR: cannot determine file type for /home/will/Dropbox/BrainformLtd/Freesurfer/October2015/YU/YUScan1/1.3.12.2.1107.5.2.36.40463.20130122101900878319572.dcm Linux localhost.localdomain 3.10.0-229.4.2.el7.x86_64 #1 SMP Wed May 13 10:06:09 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s YU exited with ERRORS at Mon Oct 12 21:21:24 NZDT 2015 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting recon-all.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)
Hi Bruce, I've attached a shot of the misalignment as seen in freeview. Yes the original images were DICOM created in Siemens machine T1, 0.8 slice thickness, can provide all DICOM tags if needed. Thanks, Will On Tue, Jan 26, 2016 at 6:00 AM, wrote: Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: mritotal failed - help with manual registration (Bruce Fischl) 2. recon -all errors (Jasmin Alves) 3. Re: Processing .mnc files (Ankita Chatterjee) 4. Re: Processing .mnc files (Bruce Fischl) 5. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg) 6. hippocampal subfields - multispectral segmentationwith FLAIR (Luigi Antelmi) 7. Re: hippocampal subfields - multispectral segmentationwith FLAIR (Eugenio Iglesias) 8. Re: recon -all errors (Bruce Fischl) 9. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl) 10. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg) 11. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl) 12. FDR map: hide very little cluster (std...@virgilio.it) 13. [All] position available immediately (Bruce Fischl) 14. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Douglas Greve) 15. Re: FDR map: hide very little cluster (Douglas Greve) 16. R: Re: FDR map: hide very little cluster (std...@virgilio.it) 17. R: Re: FDR map: hide very little cluster (std...@virgilio.it) 18. Re: R: Re: FDR map: hide very little cluster (Douglas N Greve) 19. R: R: Re: FDR map: hide very little cluster (std...@virgilio.it) 20. Re: R: R: Re: FDR map: hide very little cluster (Douglas N Greve) 21. R: Re: R: Re: FDR map: hide very little cluster (std...@virgilio.it) -- Message: 1 Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST) From: Bruce Fischl Subject: Re: [Freesurfer] mritotal failed - help with manual registration To: Freesurfer support list Message-ID: Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Will can you take the same images with freeview and send them along? Also: tell us a bit about your images. What format did they start in? Were they dicoms? Bruce On Mon, 25 Jan 2016, will brown wrote: > Hi all, > After attempting recon-all I received the error "mritotal failed, see > transforms/talairach.log" etc which I understand may have something to do > with bad output from registration. I've checked orig.mgz which does look out > of line - the orientation is off so that it appears the subject has their > head tilted off to one side (see Image1.jpg). > > I have tried to fix this manually with the help of this tutorial: > > http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview > > Hovever, the "movable" blurry image that I'm trying to line up with my > subjects image does not match the coronal, sagittal or horizontal views, > e.g. when I click "coronal" my subject is displayed correctly but the > movable image is displayed horizontally (see Image2.jpg and Image3.jpg). > > Am I missing something obvious? (and am I even on the right track given this > error?) > > Thanks in advance for any help. > > Cheers, > Will ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] The influence of cortical talairach on final surfaces
Hi all, In the freesurfer pipeline, is cortical segmentation (and the subsequent surface construction) based on the actual scans or on the scan in talairach space? Thanks, Will Brown ___ 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] Cortical gray matter surface area
Hi all, I am a little unclear as to how to find the cortical grey matter volume in the stats output files. The ?.aparc.stats file shows: Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2 What about grey? Thanks, Will ___ 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] Cortical gray matter surface area
Sorry, my mistake. I did mean surface area rather than volume. I am unsure as to how to find the total surface area of the cortical gray matter as ?.aparc.stats file only report WhiteSurfArea. Thanks, Will Message: 17 Date: Wed, 27 Aug 2014 00:48:29 -0400 From: Douglas Greve Subject: Re: [Freesurfer] Cortical gray matter surface area To: freesurfer@nmr.mgh.harvard.edu Message-ID: <53fd631d.4070...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" The volume for each structure is given as the 4th column. If you want total GM volume, look in aseg.stats doug On 8/26/14 8:43 PM, will brown wrote: > Hi all, > > I am a little unclear as to how to find the cortical grey matter > volume in the stats output files. The ?.aparc.stats file shows: > > Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2 > > What about grey? > > Thanks, > Will ___ 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] Cortical gray matter surface area
Hi all, I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info. ?.aparc.stats reports: Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2 How about the gray matter? Thanks, Will ___ 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] Cortical gray matter surface area
Thanks very much Andreia, yes this does look like what I want. I haven't had a chance to test it yet but it does indeed appear to answer my question. Thanks to those that have offered answers, to clarify, I did indeed mean the surface area of the pial surface rather than the white/grey boundary. Will On Wed, Sep 3, 2014 at 1:12 AM, <_andre...@sapo.pt> wrote: > Hi Will, > > I use the following commands to get surface area from the pial surface: > > > In the subject label dir: > > mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh. > *aparc.pial*.stats -b -a ../label/lh.aparc.annot -c > ../label/aparc.annot.ctab SUBJ lh pial > > mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh. > *aparc.pial*.stats -b -a ../label/rh.aparc.annot -c > ../label/aparc.annot.ctab SUBJ rh pial > > > > Then run aparcstats2table using *aparc.pial* instead of aparc (only > because I called this new parcellation aparc.pial) > > > > To get the total surface area of each hemisphere I use: > > In the subject stats dir: > > mris_anatomical_stats -l ../label/lh.cortex.label -f lh.*total_pial*.stats > -b SUBJ lh pial > > mris_anatomical_stats -l ../label/rh.cortex.label -f rh.*total_pial*.stats > -b SUBJ rh pial > > Then run aparcstats2table using *total_pial* instead of aparc (again, > only because I called this new parcellation total_pial. You may call it > whatever you'd like) > > > > Just remeber to leave the specified dirs when creating the tables. If you > dont't I think they will be created in the current dir. > > I use FS 5.0. > > Is this what you want? > > > Best, > Andreia > > > Citando will brown : > > Hi all, > > I messed up this question recently so just want to clarify and try again. > We want to know the cortical gray matter surface area of our subjects but > are unclear about how to get this info. > > ?.aparc.stats reports: > > Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2 > > How about the gray matter? > > Thanks, > Will > > > > > > > ___ 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] Cortical gray matter surface area
Thanks Andreia, this does appear to have worked. Please forgive my ignorance but I do just want to double check two things; 1) The first commands you have given provide the stats for the two hemispheres of the cerebral cortex only based on the pial surface, whereas the second set of commands provide the pial boundary stats for the whole brain rather than just cortex? 2) The surface area value that I am looking for (grey matter surface area at the grey/pial boundary) is listed in the new stats table next to: *# Measure Cortex, WhiteSurfArea, White Surface Total Area,* ? Thanks again, Will On Tue, Sep 9, 2014 at 5:36 PM, will brown wrote: > Thanks very much Andreia, yes this does look like what I want. I haven't > had a chance to test it yet but it does indeed appear to answer my > question. Thanks to those that have offered answers, to clarify, I did > indeed mean the surface area of the pial surface rather than the white/grey > boundary. > > Will > > > On Wed, Sep 3, 2014 at 1:12 AM, <_andre...@sapo.pt> wrote: > >> Hi Will, >> >> I use the following commands to get surface area from the pial surface: >> >> >> In the subject label dir: >> >> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f >> ../stats/lh.*aparc.pial*.stats -b -a ../label/lh.aparc.annot -c >> ../label/aparc.annot.ctab SUBJ lh pial >> >> mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f >> ../stats/rh.*aparc.pial*.stats -b -a ../label/rh.aparc.annot -c >> ../label/aparc.annot.ctab SUBJ rh pial >> >> >> >> Then run aparcstats2table using *aparc.pial* instead of aparc (only >> because I called this new parcellation aparc.pial) >> >> >> >> To get the total surface area of each hemisphere I use: >> >> In the subject stats dir: >> >> mris_anatomical_stats -l ../label/lh.cortex.label -f lh.*total_pial*.stats >> -b SUBJ lh pial >> >> mris_anatomical_stats -l ../label/rh.cortex.label -f rh.*total_pial*.stats >> -b SUBJ rh pial >> >> Then run aparcstats2table using *total_pial* instead of aparc (again, >> only because I called this new parcellation total_pial. You may call it >> whatever you'd like) >> >> >> >> Just remeber to leave the specified dirs when creating the tables. If you >> dont't I think they will be created in the current dir. >> >> I use FS 5.0. >> >> Is this what you want? >> >> >> Best, >> Andreia >> >> >> Citando will brown : >> >> Hi all, >> >> I messed up this question recently so just want to clarify and try again. >> We want to know the cortical gray matter surface area of our subjects but >> are unclear about how to get this info. >> >> ?.aparc.stats reports: >> >> Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2 >> >> How about the gray matter? >> >> Thanks, >> Will >> >> >> >> >> >> >> > > ___ 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] Cortical gray matter surface area
Thanks again, for the record, I'm using freesurfer version 5.3.0 on Centos 6. On 9/09/2014 11:00 PM, <_andre...@sapo.pt> wrote: > Hi Will, > > Just to clarify, what version of FS are you using? I think it might not be > 5.0 and I don't know if everything aplies if we are using different > versions. > > > 1) Yes, it is only based on the pial surface (and these command lines are > for the aparc, DK altas). The second set provides the surface area for each > hemisphere without including, for example, the pial surface that you see in > the hippocampus which is not accurate and one should not care about. In the > end, the second set gives you the sum of the areas in aparc, thus, you can > just make a sum of that parcellation if you want. I just realized that. > > 2) No. In the new stats file, the value that you want is at the bottom: > > # ColHeaders StructName NumVert *SurfArea* GrayVol ThickAvg ThickStd > MeanCurv GausCurv FoldInd CurvInd > > And when running aparcstats2table that's the value you should get in the > table. I think that *# Measure Cortex, WhiteSurfArea, White Surface Total > Area* may be including more stuff since it is bigger. > > > If what you want is only the total hemisphere surface area you only need > to run the second set of commands. If you want the area of each DK altas > parcellation then run the first set and then simply add them to get total > hemisphere surface area. > > > Someone from Freesurfer staff will correct me if I'm wrong. (Please) I'm > Ccing Doug since he was replying to your previous emails. > > Let's wait for their feedback. > > Andreia > > > > > Citando will brown : > > Thanks Andreia, this does appear to have worked. Please forgive my > ignorance but I do just want to double check two things; > > 1) The first commands you have given provide the stats for the two > hemispheres of the cerebral cortex only based on the pial surface, whereas > the second set of commands provide the pial boundary stats for the whole > brain rather than just cortex? > > 2) The surface area value that I am looking for (grey matter surface area > at the grey/pial boundary) is listed in the new stats table next to: *# > Measure Cortex, WhiteSurfArea, White Surface Total Area,* ? > > Thanks again, > Will > > On Tue, Sep 9, 2014 at 5:36 PM, will brown > wrote: > >> Thanks very much Andreia, yes this does look like what I want. I haven't >> had a chance to test it yet but it does indeed appear to answer my >> question. Thanks to those that have offered answers, to clarify, I did >> indeed mean the surface area of the pial surface rather than the white/grey >> boundary. >> >> Will >> >> >> On Wed, Sep 3, 2014 at 1:12 AM, <_andre...@sapo.pt> wrote: >> >>> >>> >>> >>> >>> >>> *Hi Will, I use the following commands to get surface area from the pial >>> surface: In the subject label dir:* >>> >>> >>> *mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f >>> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c >>> ../label/aparc.annot.ctab SUBJ lh pial* >>> >>> >>> *mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f >>> ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c >>> ../label/aparc.annot.ctab SUBJ rh pial * >>> >>> >>> >>> >>> >>> >>> >>> >>> *Then run aparcstats2table using aparc.pial instead of aparc (only >>> because I called this new parcellation aparc.pial) To get the total surface >>> area of each hemisphere I use: In the subject stats dir:* >>> >>> >>> *mris_anatomical_stats -l ../label/lh.cortex.label -f >>> lh.total_pial.stats -b SUBJ lh pial* >>> >>> *mris_anatomical_stats -l ../label/rh.cortex.label -f >>> rh.total_pial.stats -b SUBJ rh pial* >>> >>> *Then run aparcstats2table using total_pial instead of aparc (again, >>> only because I called this new parcellation total_pial. You may call it >>> whatever you'd like)* >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> *Just remeber to leave the specified dirs when creating the tables. If >>> you dont't I think they will be created in the current dir. I use FS 5.0. >>> Is this what you want? Best, Andreia* >>> >>> >>> >>> *Citando will brown >:* >>> >>> *
Re: [Freesurfer] Cortical gray matter surface area
Sure. We'd like to know how to find the surface area of the cortical grey matter from the pial surface. So specifically, what is the surface area of the pial/grey matter boundary of the cortex for each hemisphere? We're using Freesurfer v5.3 on Centos 6. Thanks, Will Brown On Fri, Sep 12, 2014 at 9:11 AM, Bruce Fischl wrote: > sorry, this thread has gotten too deep. Can someone summarize the question? > > > On Thu, 11 Sep 2014, _andre...@sapo.pt wrote: > > >> Ok. Then, I'm not sure if everything is correct with the command lines >> since >> I use 5.0. >> >> Any thought on this Freesurfer team? >> >> Thanks, >> Andreia >> >> Citando will brown : >> >> Thanks again, for the record, I'm using freesurfer version 5.3.0 >> on Centos 6. >> >> On 9/09/2014 11:00 PM, <_andre...@sapo.pt> wrote: >> >> Hi Will, >> >> Just to clarify, what version of FS are you using? I >> think it might not be 5.0 and I don't know if >> everything aplies if we are using different >> versions. >> >> >> 1) Yes, it is only based on the pial surface (and >> these command lines are for the aparc, DK altas). >> The second set provides the surface area for each >> hemisphere without including, for example, the pial >> surface that you see in the hippocampus which is not >> accurate and one should not care about. In the end, >> the second set gives you the sum of the areas in >> aparc, thus, you can just make a sum of that >> parcellation if you want. I just realized that. >> >> 2) No. In the new stats file, the value that you >> want is at the bottom: >> >> # ColHeaders StructName NumVert SurfArea GrayVol >> ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd >> >> And when running aparcstats2table that's the value >> you should get in the table. I think that # Measure >> Cortex, WhiteSurfArea, White Surface Total Area may >> be including more stuff since it is bigger. >> >> >> If what you want is only the total hemisphere >> surface area you only need to run the second set of >> commands. If you want the area of each DK altas >> parcellation then run the first set and then simply >> add them to get total hemisphere surface area. >> >> >> Someone from Freesurfer staff will correct me if I'm >> wrong. (Please) I'm Ccing Doug since he was replying >> to your previous emails. >> >> Let's wait for their feedback. >> >> Andreia >> >> >> >> >> >> Citando will brown : >> >> Thanks Andreia, this does appear to have >> worked. Please forgive my ignorance but >> I do just want to double check two >> things; >> >> 1) The first commands you have given provide the stats for >> the two hemispheres of the cerebral cortex only based on >> the pial surface, whereas the second set of commands >> provide the pial boundary stats for the whole brain rather >> than just cortex? >> >> 2) The surface area value that I am looking for (grey >> matter surface area at the grey/pial boundary) is listed >> in the new stats table next to: # Measure Cortex, >> WhiteSurfArea, White Surface Total Area, ? >> >> Thanks again, >> Will >> >> On Tue, Sep 9, 2014 at 5:36 PM, will brown >> wrote: >> Thanks very much Andreia, yes this does look >> like what I want. I haven't had a chance to >> test it yet but it does indeed appear to >> answer my question. Thanks to those that have >> offered answers, to clarify, I did indeed mean >> the surface area of the pial surface rather >> than the white/grey boundary. >> Will >> >> >> On Wed, Sep 3, 2014 at 1:12 AM, <_andre...@sapo.pt> >> wrote: >> >> Hi Will, >> >> I use the following commands to get >> surface area from the pial surface: >> >> >> In the subject label dir: >> >> >> mris_anatomical_stats -mgz -cortex >> ../label/lh.cortex.l
Re: [Freesurfer] Cortical gray matter surface area
Thanks Doug, Just to double check I understand you correctly, where the output says "# Measure Cortex, WhiteSurfArea, White Surface Total Area" this is now the surface area of the pial surface even though it is labeled White? Cheers, Will On Sat, Sep 13, 2014 at 3:27 AM, Douglas N Greve wrote: > > You can run something like > > cd $SUBJECTS_DIR/subject > > mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f > stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c > label/aparc.annot.ctab subject lh pial > > The "Measure Cortex" fields in the output stats/lh.aparc.pial.stats will > be measures of the pial surface as will the SurfArea, MeanCurv, GausCurv, > FoldInd, and CurvInd fields for each ROI (thickness and number of vertices > will stay the same) > > doug > > On 09/11/2014 07:29 PM, will brown wrote: > >> Sure. We'd like to know how to find the surface area of the cortical grey >> matter from the pial surface. So specifically, what is the surface area of >> the pial/grey matter boundary of the cortex for each hemisphere? >> >> We're using Freesurfer v5.3 on Centos 6. >> >> Thanks, >> Will Brown >> >> >> On Fri, Sep 12, 2014 at 9:11 AM, Bruce Fischl > <mailto:fis...@nmr.mgh.harvard.edu>> wrote: >> >> sorry, this thread has gotten too deep. Can someone summarize the >> question? >> >> >> On Thu, 11 Sep 2014, _andre...@sapo.pt <mailto:andre...@sapo.pt> >> wrote: >> >> >> Ok. Then, I'm not sure if everything is correct with the >> command lines since >> I use 5.0. >> >> Any thought on this Freesurfer team? >> >> Thanks, >> Andreia >> >> Citando will brown > <mailto:willbrown1...@gmail.com>>: >> >> Thanks again, for the record, I'm using freesurfer >> version 5.3.0 >> on Centos 6. >> >> On 9/09/2014 11:00 PM, <_andre...@sapo.pt >> <mailto:andre...@sapo.pt>> wrote: >> >> Hi Will, >> >> Just to clarify, what version of FS are you using? I >> think it might not be 5.0 and I don't know if >> everything aplies if we are using different >> versions. >> >> >> 1) Yes, it is only based on the pial surface (and >> these command lines are for the aparc, DK altas). >> The second set provides the surface area for each >> hemisphere without including, for example, the pial >> surface that you see in the hippocampus which is not >> accurate and one should not care about. In the end, >> the second set gives you the sum of the areas in >> aparc, thus, you can just make a sum of that >> parcellation if you want. I just realized that. >> >> 2) No. In the new stats file, the value that you >> want is at the bottom: >> >> # ColHeaders StructName NumVert SurfArea GrayVol >> ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd >> >> And when running aparcstats2table that's the value >> you should get in the table. I think that # Measure >> Cortex, WhiteSurfArea, White Surface Total Area may >> be including more stuff since it is bigger. >> >> >> If what you want is only the total hemisphere >> surface area you only need to run the second set of >> commands. If you want the area of each DK altas >> parcellation then run the first set and then simply >> add them to get total hemisphere surface area. >> >> >> Someone from Freesurfer staff will correct me if I'm >> wrong. (Please) I'm Ccing Doug since he was replying >> to your previous emails. >> >> Let's wait for their feedback. >> >> Andreia >> >> >> >> >> >> Citando will brown > <mailto:willbrown1...@gmail.com>>: >> >> Thanks Andreia, this does appe
[Freesurfer] CentOs 7
Hi, Is Freesurfer compatible with CentOs 7? Thanks, Will Brown ___ 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] Centos 7
Hi Zeke, I have completed a recon on CentOS 7. As far as I can see, the output matches the results from my previous recon of this subject using Freesurfer on CentOs 6. Is there any particular log that you would like to see? Will ___ 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] using T2 or flair images
Hi there, I have completed recon-all on a subject but the output is terrible. I have since found multiple series on the CD that was supplied for the subject's scan using "dcmunpack" the output was: Found 7 unique series: 1 4 5 6 7 8 9 Subject X Date 20120114 Time 082517 Institution Hagley Radiology 1 loc 1.372 5.032 30 0.9375 ROW 244.141 /home/will/Dropbox/BrainformLtd/Freesurfer/November2014/NB/NBScan1/Z01 4 T2AXIALPROP 91.82775 4500.0 90.0 0.429688 ROW 325.39062 //Z15 5 SAGT1FLAIR 7.64 2657.82 90 0.4688 ROW 195.312 //Z53 6 SAGT2FRFSE 88.272 1900 90 0.4297 ROW 122.07 //Z82 7 CORT2FLAIR 167.7 9502 90 0.4102 ROW 162.773 //Z99 8 DWIASSET 88.5 7750 90 0.8594 COL 1953.12 //Z141 9 Ax3DSWAN 22.876 38.2 15 0.4102 ROW 162.773 //Z203 I'm wondering if an expert could advise me on the best next step of progress to improve the output. I only need the pial surfaces and stats. Presumably series 1 is the T1 series? Should I use T2 also? if so which one and how? Please excuse my ignorance. Thanks, Will Brown ___ 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] inverted dicoms
Hi all, I have files that are 2D axial slices that are left-right inverted, so the left side of the brain is on the right side of each slice. Do I need to do anything to the dicoms before importing them into freesurfer? Thanks, Will ___ 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] mritotal failed
Hi there, I am receiving the following error during recon-all: mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.7573/src.mnc transforms/talairach.auto.xfm Can't locate shellwords.pl in @INC (@INC contains: /usr/local/freesurfer/mni/bin/../lib/mni_autoreg /usr/local/freesurfer/mni/lib/perl5/5.8.5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /usr/local/freesurfer/mni/bin/mritotal line 460. ERROR: mritotal failed, see transforms/talairach.log Any ideas? /usr/local/freesurfer/subjects/KR/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux localhost.localdomain 3.10.0-123.9.3.el7.x86_64 #1 SMP Thu Nov 6 15:06:03 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Thu Nov 13 14:48:33 NZDT 2014 tmpdir is transforms/tmp.talairach.7573 /usr/local/freesurfer/subjects/KR/mri mri_convert orig_nu.mgz transforms/tmp.talairach.7573/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.7573/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=1430.00, TE=3.62, TI=1100.00, flip angle=15.00 i_ras = (-1, 7.45058e-09, 1.86265e-09) j_ras = (3.72529e-09, -5.96046e-08, -1) k_ras = (-1.49012e-08, 1, 0) writing to transforms/tmp.talairach.7573/src.mnc... [will@localhost.localdomain:/usr/local/freesurfer/subjects/KR/mri] [2014-11-13 14:48:33] running: /usr/local/freesurfer/mni/bin/mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.7573/src.mnc transforms/talairach.auto.xfm ___ 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] Data requirements
Hi all, I have structural data that has a slice thickness of 5mm and spacing between slices of 5mm (there are around 30 dicom images). I ran it through recon-all but the output was bad. Is it possible to create surfaces from such data? Or is the bad output the answer to this question... Thanks, Will ___ 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] Dicom from CT
Hi all, I only have experience processing dicom images from MRI. Can Freesurfer handle images from CT as well? Anything to note? Thanks, Will ___ 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] Dicom from CT
Sorry, yes we would like to calculate some volume statistics and surfaces models. Thanks, Will Message: 8 Date: Fri, 05 Dec 2014 15:42:16 -0500 From: Douglas N Greve Subject: Re: [Freesurfer] Dicom from CT To: freesurfer@nmr.mgh.harvard.edu Message-ID: <548218a8.7020...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed What do you mean by "handle"? You cannot run it through the anatomical analysis if that is what you mean. doug On 12/05/2014 03:38 PM, will brown wrote: > Hi all, > > I only have experience processing dicom images from MRI. Can > Freesurfer handle images from CT as well? Anything to note? > > Thanks, > Will > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 ___ 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.
