Re: [Freesurfer] Need Help
Thanks a lot. It helped. > On May 25, 2016, at 3:24 PM, Douglas N Greve > wrote: > > recon-all -s yoursubjectname -i /path/to/one/dicomfile.dcm > tksurfer yoursubjectname lh pial -ov > $SUBJECTS_DIR/yoursubjectname/surf/lh.thickness -fminmax .1 3 > > > On 05/24/2016 08:34 PM, HARI GURAGAIN wrote: >> Hello, >> >> I am kind of new to the neuroimaging. I was trying to reproduce the >> following type of figure in freesurfer (3d image with thickness). But >> I couldn’t do that. Is it possible for anyone to explain how to >> generate such figure from mri data. Just to clarify, I have the mri >> data in the form of *.dcm. Is there any specific command to get >> through it? I tried to work on similar figures using tksurfer *** but >> couldn’t produce. >> >> Your help is greatly appreciated. >> Thank you, >> >> Hari >> unknown.tiff >> This figure is from one paper. >> Fig. 4. 3D models of the pial surfaces generated by FreeSurfer with a >> colored overlay of the local cortical thickness in mm. The top row >> shows the pial surfaces of the left and right >> hemisphere based on data with an isotropic resolution of 0.5 mm and >> the bottom row with an isotropic resolution of 1 mm; both data sets >> have been acquired at 7 T. >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Coregister the CT image and MRI image
Dear Freesurfer community, I am relatively new to this community. I was trying to register the CT image and the MRI images (MRI as a the target volume and CT as the movable volume). I used the mri_robust_register to to do the registration as below: mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit The problem is that: after register, the new image (v1to2.nii) is not exactly aligned with the original MRI image (vol2.nii). It gives a very different output. I wonder if I am missing anything here or I need to do some extra steps after the above command in order to get the correct alignment of the two images. I was hoping to get the resultant image should be well orient with the target volume image (vol2.nii image in my case). I really appreciate any help here. Hari Guragain ___ 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] Coregister the CT image and MRI image
Thank you Douglas. One more thing: Is there any syntax how to use it? I wonder if it is same as the mri_robust_register? > On Jun 9, 2016, at 3:43 PM, Douglas N Greve wrote: > > I don't think robust register will do cross-modal. You may be better off > using mri_coreg, which you can get from here > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg > > > On 06/09/2016 01:58 PM, HARI GURAGAIN wrote: >> Dear Freesurfer community, >> >> I am relatively new to this community. >> >> I was trying to register the CT image and the MRI images (MRI as a the >> target volume and CT as the movable volume). I used the >> mri_robust_register to to do the registration as below: >> >> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta >> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit / >> >> The problem is that: after register, the new image (v1to2.nii) is not >> exactly aligned with the original MRI image (vol2.nii). It gives a >> very different output. I wonder if I am missing anything here or I >> need to do some extra steps after the above command in order to get >> the correct alignment of the two images. I was hoping to get the >> resultant image should be well orient with the target volume image >> (vol2.nii image in my case). >> >> I really appreciate any help here. >> >> Hari Guragain >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Coregister the CT image and MRI image
Dear Douglas, The executable is not working as it says ‘Library not loaded: @executable_path/../lib/gcc/lib/libgomp.1.dylib’ Referenced from: /Applications/freesurfer/bin/mri_coreg.mac Reason: image not found Trace/BPT trap:5 I am currently using the freeview: Version 1.0 and the operating system is: OS X EI Captain Version: 10.11.5 I wonder if the file you pointed works for the mac? Should I reinstall the freeview? Any help would be greatly appreciated. Thank you, Hari > On Jun 9, 2016, at 4:28 PM, Douglas N Greve wrote: > > No, it is not the same command line. If you run it without args, it will > give you some info, but it is basically > > mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta > > > On 06/09/2016 05:22 PM, HARI GURAGAIN wrote: >> Thank you Douglas. >> One more thing: Is there any syntax how to use it? I wonder if it is same as >> the mri_robust_register? >> >> >>> On Jun 9, 2016, at 3:43 PM, Douglas N Greve >>> wrote: >>> >>> I don't think robust register will do cross-modal. You may be better off >>> using mri_coreg, which you can get from here >>> >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg >>> >>> >>> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote: >>>> Dear Freesurfer community, >>>> >>>> I am relatively new to this community. >>>> >>>> I was trying to register the CT image and the MRI images (MRI as a the >>>> target volume and CT as the movable volume). I used the >>>> mri_robust_register to to do the registration as below: >>>> >>>> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta >>>> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit / >>>> >>>> The problem is that: after register, the new image (v1to2.nii) is not >>>> exactly aligned with the original MRI image (vol2.nii). It gives a >>>> very different output. I wonder if I am missing anything here or I >>>> need to do some extra steps after the above command in order to get >>>> the correct alignment of the two images. I was hoping to get the >>>> resultant image should be well orient with the target volume image >>>> (vol2.nii image in my case). >>>> >>>> I really appreciate any help here. >>>> >>>> Hari Guragain >>>> >>>> >>>> >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Coregister the CT image and MRI image
Dear Douglas, I have used the same file as you pointed, but it keeps on showing the same error message. I copied the file to my /Applications/freesurfer/bin directory but it still shows the same error message: >> ‘dyld: Library not loaded: @executable_path/../lib/gcc/lib/libgomp.1.dylib’ >> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac >> Reason: image not found >> Trace/BPT trap:5 Does it have something to do with the library issue with mac? Any help is appreciated. Thank you, > On Jun 9, 2016, at 5:45 PM, Douglas N Greve wrote: > > try > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac > > > > On 06/09/2016 06:21 PM, HARI GURAGAIN wrote: >> Dear Douglas, >> >> The executable is not working as it says ‘Library not loaded: >> @executable_path/../lib/gcc/lib/libgomp.1.dylib’ >> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac >> Reason: image not found >> Trace/BPT trap:5 >> >> I am currently using the freeview: Version 1.0 and the operating system is: >> OS X EI Captain Version: 10.11.5 >> I wonder if the file you pointed works for the mac? Should I reinstall the >> freeview? >> Any help would be greatly appreciated. >> >> Thank you, >> >> Hari >> >> >>> On Jun 9, 2016, at 4:28 PM, Douglas N Greve >>> wrote: >>> >>> No, it is not the same command line. If you run it without args, it will >>> give you some info, but it is basically >>> >>> mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta >>> >>> >>> On 06/09/2016 05:22 PM, HARI GURAGAIN wrote: >>>> Thank you Douglas. >>>> One more thing: Is there any syntax how to use it? I wonder if it is same >>>> as the mri_robust_register? >>>> >>>> >>>>> On Jun 9, 2016, at 3:43 PM, Douglas N Greve >>>>> wrote: >>>>> >>>>> I don't think robust register will do cross-modal. You may be better off >>>>> using mri_coreg, which you can get from here >>>>> >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg >>>>> >>>>> >>>>> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote: >>>>>> Dear Freesurfer community, >>>>>> >>>>>> I am relatively new to this community. >>>>>> >>>>>> I was trying to register the CT image and the MRI images (MRI as a the >>>>>> target volume and CT as the movable volume). I used the >>>>>> mri_robust_register to to do the registration as below: >>>>>> >>>>>> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta >>>>>> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit / >>>>>> >>>>>> The problem is that: after register, the new image (v1to2.nii) is not >>>>>> exactly aligned with the original MRI image (vol2.nii). It gives a >>>>>> very different output. I wonder if I am missing anything here or I >>>>>> need to do some extra steps after the above command in order to get >>>>>> the correct alignment of the two images. I was hoping to get the >>>>>> resultant image should be well orient with the target volume image >>>>>> (vol2.nii image in my case). >>>>>> >>>>>> I really appreciate any help here. >>>>>> >>>>>> Hari Guragain >>>>>> >>>>>> >>>>>> >>>>>> ___ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> gr...@nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> ___ >>>>> Freesurfer mailing l
Re: [Freesurfer] Coregister the CT image and MRI image
Dear Douglas, With the suggestions from Zeke, the mri_coreg is working now. I have one last question: I got the new v1to2.lta. How to apply this transformation to the CT image? Is it by using mri_convert? Something like below? mri_convert -at v1to2.lta CT.nii new_CT.nii Any suggestion will be greatly appreciated. Thank you again, Hari Guragain > On Jun 9, 2016, at 5:53 PM, HARI GURAGAIN wrote: > > Dear Douglas, > > I have used the same file as you pointed, but it keeps on showing the same > error message. I copied the file to my /Applications/freesurfer/bin directory > but it still shows the same error message: >>> ‘dyld: Library not loaded: @executable_path/../lib/gcc/lib/libgomp.1.dylib’ >>> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac >>> Reason: image not found >>> Trace/BPT trap:5 > > > Does it have something to do with the library issue with mac? > Any help is appreciated. > Thank you, > > >> On Jun 9, 2016, at 5:45 PM, Douglas N Greve >> wrote: >> >> try >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac >> >> >> >> On 06/09/2016 06:21 PM, HARI GURAGAIN wrote: >>> Dear Douglas, >>> >>> The executable is not working as it says ‘Library not loaded: >>> @executable_path/../lib/gcc/lib/libgomp.1.dylib’ >>> Referenced from: /Applications/freesurfer/bin/mri_coreg.mac >>> Reason: image not found >>> Trace/BPT trap:5 >>> >>> I am currently using the freeview: Version 1.0 and the operating system is: >>> OS X EI Captain Version: 10.11.5 >>> I wonder if the file you pointed works for the mac? Should I reinstall the >>> freeview? >>> Any help would be greatly appreciated. >>> >>> Thank you, >>> >>> Hari >>> >>> >>>> On Jun 9, 2016, at 4:28 PM, Douglas N Greve >>>> wrote: >>>> >>>> No, it is not the same command line. If you run it without args, it will >>>> give you some info, but it is basically >>>> >>>> mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta >>>> >>>> >>>> On 06/09/2016 05:22 PM, HARI GURAGAIN wrote: >>>>> Thank you Douglas. >>>>> One more thing: Is there any syntax how to use it? I wonder if it is same >>>>> as the mri_robust_register? >>>>> >>>>> >>>>>> On Jun 9, 2016, at 3:43 PM, Douglas N Greve >>>>>> wrote: >>>>>> >>>>>> I don't think robust register will do cross-modal. You may be better off >>>>>> using mri_coreg, which you can get from here >>>>>> >>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg >>>>>> >>>>>> >>>>>> On 06/09/2016 01:58 PM, HARI GURAGAIN wrote: >>>>>>> Dear Freesurfer community, >>>>>>> >>>>>>> I am relatively new to this community. >>>>>>> >>>>>>> I was trying to register the CT image and the MRI images (MRI as a the >>>>>>> target volume and CT as the movable volume). I used the >>>>>>> mri_robust_register to to do the registration as below: >>>>>>> >>>>>>> /mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta >>>>>>> --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit / >>>>>>> >>>>>>> The problem is that: after register, the new image (v1to2.nii) is not >>>>>>> exactly aligned with the original MRI image (vol2.nii). It gives a >>>>>>> very different output. I wonder if I am missing anything here or I >>>>>>> need to do some extra steps after the above command in order to get >>>>>>> the correct alignment of the two images. I was hoping to get the >>>>>>> resultant image should be well orient with the target volume image >>>>>>> (vol2.nii image in my case). >>>>>>> >>>>>>> I really appreciate any help here. >>>>>>> >>>>>>> Hari Guragain >>>>>>> >>>>>>> >>>>>>> >>>>>>> ___ >>>>>>> Freesurfer mailing lis
[Freesurfer] Using Freesurfer commands in matlab
Dear Freesurfer, I am using the new development version of freesurfer ( ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev). I am trying to call some of the freesurfer commands like: mri_coreg or some other. When I use the something like the following in Matlab: command='/Applications/freesurfer/bin/mri_coreg' and the below: [status,cmdout]=system(command) It is showing a weird error message like below: ### dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib ### I really don't understand why this error is coming. I have seen people have used the mri_*** commands a lot of times in matlab but unfortunately, it shows the above error in my case. Is it the error from Matlab, freesurfer, mac or something else? Any help in solving this issue will be greatly appreciated. Thank you. ___ 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] Problem while using the -localGI
Dear Freesurfer experts, I am having trouble using the -localGI option to smoothen the pial surface. When I use the command like: recon-all -s ABC -localGI I got the following error: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-OSX-dev-20160611-876a0e6 cp: /Applications/freesurfer/subjects/ABC/scripts/lastcall.build-stamp.txt: Permission denied INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer /Applications/freesurfer/subjects/ABC/scripts/recon-all.cmd: Permission denied. But when I tried to do the same reconstruction via the super user(su), it says something about the library linking like below. I am wondering if it is a problem related to Matlab or freesurfer? I am currently using the development version of freesurfer. Any help will be greatly appreciated. reading surface from lh.pial... dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Thank you all. Hari ___ 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] fornix segmentation using recon-all
Dear Freesurfer Experts, I am interested to get the volume information of the structure "fornix" in the aseg.stats file. I would appreciate if there is any such argument that can be used along with the recon-all to get the volume information of the fornix like below. Till now, I have been using · *recon-all -autorecon-all -subjid **your_subject_name* Any suggestions will be appreciated. # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 4 6489 6958.2 Left-Lateral-Ventricle34.8514 11.576715.82.67. Thank you, Hari Guragain ___ 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] fornix segmentation using recon-all
Dear Bruce, When I used the mri_cc command and used the -f and -force options, I could see the fornix.mgz file. I wonder how can I get the volume in mm^3 of the structure "fornix" from the above file? I couldn't see the volume of fornix in the aseg.stat file. It would be great if I could find the volume of both left and right fornix. Thank you in advance for help. Hari Guragain, On Fri, Jul 8, 2016 at 11:38 AM, Bruce Fischl wrote: > Hi Hari > > if you include the -f flag to mri_cc it will include the fornix in the cc > segmentation. We haven't tested it a ton so I'm not sure how well it will > work on your data, but give it a try > > cheers > Bruce > > > > On Thu, 7 Jul 2016, Hari Guragain wrote: > > Dear Freesurfer Experts, >> I am interested to get the volume information of the structure "fornix" >> in the aseg.stats file. >> I would appreciate if there is any such argument that can be used along >> with the recon-all to get the volume information of the fornix like below. >> Till now, >> I have been using >> >> · recon-all -autorecon-all -subjid your_subject_name >> >> >> Any suggestions will be appreciated. >> >> >> # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean >> normStdDev normMin normMax normRange >> 1 4 6489 6958.2 Left-Lateral-Ventricle34.8514 >> 11.576715.82.67. >> >> Thank you, >> >> Hari Guragain >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Hippocampal Subfields for T2-FLAIR images
Dear Freesurfer community, I am trying to get the segmentation of hippocampal subfields by using the development version of the freesurfer. I have few normals with T2-FLAIR images along with T1 whose subfield volume needs to be calculated. I am wondering if the algorithm that calculate the hippocampal subfields can handle the T2-FLAIR? According to the wiki ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields), it can handle the T2 but didn't say anything about the T2-FLAIR. It would be great if someone clarify this. Thank you, Hari Guragain ___ 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] ERROR: make_roi_paths did not complete successfully!
Hi Freesurfer experts, I was working on to conduct the local gyrification index analysis. I am getting the following error message when I used the option -localGI in recon-all. Improper assignment with rectangular empty matrix. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); ERROR: make_roi_paths did not complete successfully! I have seen people have similar problem long time ago ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33701.html). I also tried to check the SearchProjectionOnPial.m file and it looks same as what was attached in the email. Can anyone help on this? I will really appreciate. Thank you, Hari ___ 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] ERROR: mritotal failed, see transforms/talairach.log
Hi Freesurfer Community, I was trying to run the recon-all for one of the subjects. I got following error message: "ERROR: mritotal failed, see transforms/talairach.log". The image seems to have some missing hippocampal area. I wonder If we can still run the recon-all? I checked previous archive emails ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40166.html). It says tkregister can be used to manually align the image. Can anyone explain properly, how can we use the tkregister to align the image and save so that the freesurfer cannot complain about the "mritotal failed". Thank you in advance, Hari ___ 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.
