Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

ROI statistics and median values
by Helen Beaumont 18 Jan '18

18 Jan '18

I can use mri_segstats to get mean and std dev for values within a segmented image. Is there any way I can get median values?

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why freesurfer is not able to segment frontal cortex
by Vidhu Agrawal 18 Jan '18

18 Jan '18

Does freesurfer segments frontal cortex? If yes the how we can do that I have tried to do it by using the command :mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_superior.nii --match 1156 mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_inferior.nii --match 1154 mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_middle.nii --match 1156 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_operacula.nii --match 1106 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_orbital.nii --match 1107 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_triangula.nii --match 1108 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_middle.nii --match 1109 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_superior.nii --match 1110 but it is not segmenting any region Looking forward for your reply. Thanking you With regards vidhu agarwal

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Re: [Freesurfer] Visualisation left and right hemisphere
by Douglas Greve 18 Jan '18

18 Jan '18

Hi Ahmad, you can use mris_left_right_register to register the left and right hemis, then mris_apply_reg to map the left annot to the right (or other way around). ps. please remember to post to the FS list. Thanks! On 1/17/18 9:13 AM, Ahmad Mheich wrote: > /Hello, / > // > /Is it possible to combine the lh and rh annotation files into a > single //annotation file for visualisation? How? / > /Best regards/ > /Ahmad/

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Re: [Freesurfer] Issues with hippo subfields / amygdala fixed
by Maksimovskiy, Arkadiy 17 Jan '18

17 Jan '18

Got it. Thank you so much for all the information. Best, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Re: [Freesurfer] Hippocampal Sub-field volume units
by Iglesias Gonzalez, Eugenio 17 Jan '18

17 Jan '18

Short answer: yes, it’s cubic mm. -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Crawford, Anna" <CRAWFOA4(a)ccf.org> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 17 January 2018 at 19:20 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal Sub-field volume units Hello, i am using the hippocampal subfield segmentation. I am looking at the results in [lr]h.hippoSfVolumes-T1.v10.txt. I saw the following in the FAQs and was unsure of what the units were then in the .txt file. Does the .txt file give units in mm^3? * The sum of the number of voxels of a given structure multiplied by the volume of a voxel is not equal to the volume reported in [lr]h.hippoSfVolumes*.txt. This is because the volumes are computed upon a soft segmentation, rather than the discrete labels in [lr]h.hippoSfLabels*.mgz. This is the same that happens with the main recon-all stream: if you compute volumes by counting voxels in aseg.mgz, you don't get the values reported in aseg.stats. Thank you, Anna =================================== Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Hippocampal Sub-field volume units
by Crawford, Anna 17 Jan '18

17 Jan '18

Hello, i am using the hippocampal subfield segmentation. I am looking at the results in [lr]h.hippoSfVolumes-T1.v10.txt. I saw the following in the FAQs and was unsure of what the units were then in the .txt file. Does the .txt file give units in mm^3? * The sum of the number of voxels of a given structure multiplied by the volume of a voxel is not equal to the volume reported in [lr]h.hippoSfVolumes*.txt. This is because the volumes are computed upon a soft segmentation, rather than the discrete labels in [lr]h.hippoSfLabels*.mgz. This is the same that happens with the main recon-all stream: if you compute volumes by counting voxels in aseg.mgz, you don't get the values reported in aseg.stats. Thank you, Anna =================================== Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Issues with hippo subfields / amygdala fixed
by Maksimovskiy, Arkadiy 17 Jan '18

17 Jan '18

Dear Dr. Iglesias, Could you please let me know what the specific problems were that are fixed? I am asking because I have already applied this segmentation, and want to make sure that the data is valid. Thank you so much, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Cloning Voxel Tool Question
by Maksimovskiy, Arkadiy 17 Jan '18

17 Jan '18

Hi All, I was wondering if someone might be able to confirm about whether cloning a voxel is working right based on my description. My concern stems from the fact that when I follow instructions to clone a voxel from a T1 onto the brainmask, I click on the brainmask but do not see any immediate indication that the voxel(s) have been cloned. This is unlike erasing voxels, when the immediate indication is the brainmask dissappearing within the area that is erased. I was wondering if someone imght be able to confirm (1) whether this is normal and (2) whether there is no way to see if the voxel has been cloned prior to rerunning the reconstruction script with the incorporated edits. Thank you for your help, Arkadiy

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Issues with hippo subfields / amygdala fixed
by Iglesias Gonzalez, Eugenio 17 Jan '18

17 Jan '18

Dear all, The problems with the hippocampal subfield / nuclei of amygdala module (as well as with the brainstem module) in the dev version should now be fixed. I apologize for the inconvenience these issues might have caused. I rushed to leave everything ready right before the winter break and made a mistake when committing files to the repository. I have also updated the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures Thanks for the patience, Eugenio PS: if anyone has success stories with the new tail/body/head segmentation of the hippocampus, please share them with me! -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

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Freesurfer compilation for supporting cuda9.1
by zuxfoucault Wong 17 Jan '18

17 Jan '18

Hi Freesurfers, I tried different ways to compile freesurfer for support cuda 9.1. Unfortunately, I still cannot get it work. While I tried to compile a specific module freesurfer/utils where the errors generated, I got the error message. Any suggestions would be appreciated! gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I../include/dicom -I../xml2 -I../include/NrrdIO -DTEEM_DIO=0 -DTEEM_32BIT=0 -DTEEM_QNANHIBIT=1 -DTEEM_ENDIAN=1234 -I../jpeg -I../tiff -I../expat -I/home/bc/software /environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit -I/home/bc/softwa re/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/Algorithms -I/h ome/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/Ba sicFilters -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/In sightToolkit/Common -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/i nclude/InsightToolkit/IO -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/curr ent/include/InsightToolkit/Numerics -I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packag es/itk/current/include/InsightToolkit/Numerics/Statistics -I/home/bc/software/environment/freesurfer_src /centos6-x86_64-packages/itk/current/include/InsightToolkit/Review -I/home/bc/software/environment/frees urfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/Review/Statistics -I/home/bc/softwa re/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit/SpatialObject - I/home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/itk/current/include/InsightToolkit /Utilities -DHAVE_ITK_LIBS -I../glut -DHAVE_GLUT_LIBS -I/home/bc/software/environment/freesurfer_src/c entos6-x86_64-packages/vxl/current/include/vxl/core -I/home/bc/software/environment/freesurfer_src/cento s6-x86_64-packages/vxl/current/include/vxl/vcl -I/home/bc/software/environment/freesurfer_src/centos6-x8 6_64-packages/vxl/current/include/vxl/v3p/netlib -I/home/bc/software/environment/freesurfer_src/centos6- x86_64-packages/vxl/current/include/vxl/v3p/netlib/opt -I/usr/local/cuda/include -DHAVE_ZLIB -g -O3 -mss e2 -mfpmath=sse -Wall -Wno-unused-but-set-variable -DUSE_SSE_MATHFUN -fopenmp -DHAVE_OPENMP -m64 -DLinx -DANSI -fdata-sections -ffunction-sections -Wl,--gc-sections -I/home/bc/software/environment/freesurfe r_src/centos6-x86_64-packages/mni/current/include -DFS_CUDA -I/usr/local/cuda/include -MT libutils_cud a_a-mrishash.o -MD -MP -MF .deps/libutils_cuda_a-mrishash.Tpo -c -o libutils_cuda_a-mrishash.o `test -f 'mrishash.c' || echo './'`mrishash.c mrifilter.c: In function ‘MRIconvolveGaussian’: mrifilter.c:2618:7: error: ‘width’ undeclared (first use in this function) if (width <= 1 || height <= 1 || depth <= 1) ^ mrifilter.c:2618:7: note: each undeclared identifier is reported only once for each function it appears in mrifilter.c:2618:21: error: ‘height’ undeclared (first use in this function) if (width <= 1 || height <= 1 || depth <= 1) ^ mrifilter.c:2618:36: error: ‘depth’ undeclared (first use in this function) if (width <= 1 || height <= 1 || depth <= 1) ^ Makefile:4419: recipe for target 'libutils_cuda_a-mrifilter.o' failed make[3]: *** [libutils_cuda_a-mrifilter.o] Error 1 make[3]: *** Waiting for unfinished jobs.... mv -f .deps/libutils_cuda_a-mriprob.Tpo .deps/libutils_cuda_a-mriprob.Po mv -f .deps/libutils_cuda_a-mrisbiorthogonalwavelets.Tpo .deps/libutils_cuda_a-mrisbiorthogonalwavelets. Po mv -f .deps/libutils_cuda_a-mrisegment.Tpo .deps/libutils_cuda_a-mrisegment.Po mv -f .deps/libutils_cuda_a-mrishash.Tpo .deps/libutils_cuda_a-mrishash.Po mv -f .deps/libutils_cuda_a-mrinorm.Tpo .deps/libutils_cuda_a-mrinorm.Po mv -f .deps/libutils_cuda_a-mripolv.Tpo .deps/libutils_cuda_a-mripolv.Po mv -f .deps/libutils_cuda_a-mriset.Tpo .deps/libutils_cuda_a-mriset.Po make[3]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer/utils' Makefile:6230: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer/utils' Makefile:1060: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer' Makefile:970: recipe for target 'all' failed make: *** [all] Error 2 Best, Foucault

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