Freesurfer

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30088 discussions

T2 seq. for hippocampus ??
by Anik Dar 25 Jun '19

25 Jun '19

External Email - Use Caution Hi All, I have 1x1x3 cubic mm T2 and 1x1x1 cubic mm FLAIR, in addition to 1x1x1 cubic mm MPRAGE. Can you please let me know whether I should use only T1 or should I use one of the additional seq. for hippocampal subfield segmentation ? cheers Nik

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Re: [Freesurfer] Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors
by David S Lee 25 Jun '19

25 Jun '19

External Email - Use Caution Hello Bruce, Thanks for responding back. To your question RE: "what does the aseg look like in those cases? That is, is it the hippo/amygdala stuff failing or is the root cause further back in the stream (something that caused a bad aseg)" In all 5 cases I mentioned, ASEG looks fine. In other words, ASEG masks for both Amygdala and Hippocampus cover the appropriate voxels relative to subjects' T1 space. However, in all cases (116 subjects I looked at) the latest subfield segmentation seem to *underestimate these regions, meaning ASEG always covers more voxels. Along those lines, large portions of AAA regions are usually marked as "Cerebral Cortex" in ASEG. And the biggest issue again is that though AAA for 3 subjects are not visible in subfield segmentation mask, I get volumetric output. In one case *(Screenshot attached)*, R AAA has single voxel allocated, yet the volume is greater than the Left side which covers more space. Also for the 2 cases in which medial nuclei are marked as Putamen *(Screenshot attached)*, ASEG of putamen and amygdala looks good, but the problematic voxels are darker compared to neighboring voxels *(Screenshot attached)*. This could be tissue damage and/or incorrect identification of "vessel". What would be your recommendation to resolve these issues? Thanks for your time, -- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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Different aparc values
by vittal korann 25 Jun '19

25 Jun '19

External Email - Use Caution Hello FreeSurfer experts, I'm planning to run QDEC on Schizophrenia and controls. To do that I ran recon-all for few subjects in 2 different systems. Both systems have ubuntu 16.04 OS but different freesurfer versions. One is using FS version6 and other is FS version5.3. Just for confirmation, I ran recon-all for the same subjects in 2 above said systems. Now both yield different values for the area. Here I have tabulated the values: fsid Left-Lateral-Ventricle Left-Inf-Lat-Vent Left-Cerebellum-White-Matter Left-Cerebellum-Cortex Left-Thalamus-Proper Left-Caudate Left-Putamen Left-Pallidum 3rd-Ventricle 4th-Ventricle Brain-Stem Left-Hippocampus Left-Amygdala CSF Left-Accumbens-area Left-VentralDC Left-choroid-plexus Right-Lateral-Ventricle Right-Inf-Lat-Vent Right-Cerebellum-White-Matter Right-Cerebellum-Cortex Right-Thalamus-Proper Right-Caudate Right-Putamen Right-Pallidum Right-Hippocampus Right-Amygdala Right-Accumbens-area Right-VentralDC Right-choroid-plexus WM-hypointensities Optic-Chiasm CC_Posterior CC_Mid_Posterior CC_Central CC_Mid_Anterior CC_Anterior INSP015 16157.6 1227.3 11526.1 50572.8 6893 3228.3 5076.3 1927.7 2698.1 2577.8 17706.7 3525.3 1594.6 1164.3 538 4063.9 889.6 10616.9 1179.4 10638.1 50615.7 7252.9 3612.1 5719.7 1788.7 3852.7 1980.1 504.5 3762.4 748.8 728.9 194.4 854.8 393.8 393.9 425.8 1042.1 INSP015 16157.6 1227.3 11526.1 50572.8 6893 3228.3 5076.3 1927.7 2698.1 2577.8 17706.7 3525.3 1594.6 1164.3 538 4063.9 889.6 10616.9 1179.4 10638.1 50615.7 7252.9 3612.1 5719.7 1788.7 3852.7 1980.1 504.5 3762.4 748.8 728.9 194.4 854.8 393.8 393.9 425.8 1042.1 INSP019 7059.6 296 10820.8 42288.3 6177.2 2785.3 4573.8 1793.4 1283.5 1819.9 18958.5 3546.9 1535.8 1212.9 471.2 3741.7 583.6 7378.3 249.5 10200.6 42803.5 6173.9 3078.5 4617.6 1861.3 3638 1599.3 473.7 3532.6 627.1 591.4 270.3 897.7 443.6 497.5 460.7 798.9 INSP019 6962.9 288.8 11995 44004.4 6471.6 2883.8 4653 1888.6 1285.7 1706.1 18983.8 3619.9 1515.5 1117 493.8 3790.8 620.7 7446.8 273.6 10674.7 42678.1 6220.8 3109.2 4498.1 1943 3540.7 1658.3 499.8 3656.3 652 735.6 189.4 863.6 470.6 434.4 502.6 749.1 IYBA009 10661.7 644 16029.1 61364.8 7534.2 4416.4 5562.8 2279.9 1335.2 1775.6 24381.2 3787.8 1666.3 970.4 624.4 4286.9 709.1 9079.2 803.7 15172.2 59565.1 6989.7 4334.1 5550.7 2267.8 3928.2 1743.1 582.4 4465.2 676.6 728 195.6 667.6 426.8 363.9 362.4 929.1 IYBA009 10730.6 722.5 16662.8 60503.6 7686.1 4328.3 5430.1 2256.9 1365 1720.2 24139.9 3749.1 1635.9 995.6 639.8 4374 573.9 8963.9 795.2 15817.6 60176.1 7044.7 4251.9 5423.8 2241.1 3715.8 1749.2 600.2 4418.1 623.8 953.8 155 664.6 444.3 401.5 370.4 924.9 The above variation is because of different versions or each time freesurfer yields different values? Could you please educate me more on this. Because if the freesurfer version is the issue then I need to run all analysis in one system which will take a lot of time. Thanks & regards Vittal

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Re: [Freesurfer] DesikanKilliany ROI for mri_glmfit
by Greve, Douglas N.,Ph.D. 24 Jun '19

24 Jun '19

Try running it wiith --help to get docs and examples On 6/24/19 4:52 PM, Tammi Kral wrote: > > External Email - Use Caution > > This may be a naïve question - but this function > (mri_annotation2label) appears to be for use with individual subject > data - how do I use it with the DK atlas? When I provide the DK atlas > file as the "subject" input I get an error because it is looking for a > standard subject directory structure with the normal files (e.g. in > 'surf'). > > > Or am I creating a label for each individual subject to reference with > mri_glmfit? > > ------------------------------------------------------------------------ > *From:* Tammi Kral > *Sent:* Friday, June 21, 2019 9:18:46 PM > *To:* Greve, Douglas N.,Ph.D. > *Subject:* Re: [Freesurfer] DesikanKilliany ROI for mri_glmfit > > Thank you, I will try what you have suggested. Yes, it is a > surface-based analysis. > > ------------------------------------------------------------------------ > *From:* Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> > *Sent:* Friday, June 21, 2019 7:12:26 PM > *To:* Tammi Kral > *Subject:* Re: [Freesurfer] DesikanKilliany ROI for mri_glmfit > Can you give more information? Eg, is this a surface-based or > volume-based study? If you are doing a surface-based and want to > confine the results to the insula, then you can use > mri_annotation2label to break the DK atlas into individual labels, > then pass the insula label to mri_glmfit through the --label option. > > On 6/19/2019 4:32 AM, Tammi Kral wrote: >> >> External Email - Use Caution >> >> Hello, >> >> >> I would like to use the insula label/ROI from the DesikanKilliany >> atlas with mri_glmfit. How do I reference this label, as I don't see >> a LUT for this atlas. >> >> >> I appreciate any suggestions. >> >> >> Thanks, >> >> >> Tammi R.A. Kral, M.S. >> -- >> Doctoral Candidate, Psychology >> University of Wisconsin-Madison >> Center for Healthy Minds >> Waisman Brain Imaging Laboratory >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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base frame respectively reference frame for computation of FS-FAST motion parameters
by Pfannmoeller, Joerg Peter 24 Jun '19

24 Jun '19

Hello, as far as I can see FS-FAST uses the 0th frame as the reference frame in the computation of the motion parameters using the function . However, in the visualization of the translations the motion parameters seem to use the middle frame as the reference point. Is this the case? What is the motivation for setting the base frame to the first frame? Best Joerg

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I have a question for "matlabruntime"
by Gwang-Won Kim 24 Jun '19

24 Jun '19

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Unanswered question regarding including covariates in the fsgd file and the contrast matrix
by Basavaraju, Rakshathi 24 Jun '19

24 Jun '19

External Email - Use Caution Hi all FS users, I have the basic doubt of including age and gender as co-variates for a cortical thickness comparison between 2 groups. I read extensively many mails answering these questions but still could not get a satisfactory answer for the question. As I have 2 discrete variables i.e. Group with 2 levels and gender with 2 levels and one continuous variable of age my contrast matrix should be like this: [0 0 0 0 0 0 0 0] which is [malegroup1 femalegroup1 malegroup2 femalegroup2 age.malegroup1 age.femalegroup1 age.malegroup2 age.femalegroup2] I understood that if I have to test the effect of only the groups my contrast matrix should be: [0.5 0.5 -0.5 -0.5 0 0 0 0] What should be my contrast matrix if I have to include age and gender as covariates respectively? I know gender cannot be included as columns of 1s and 0s by my reading of previous mails. In one of the mail I read that if we want to test for interaction of group and gender (disregarding effect of age) the contrast matrix file should be: [0.5 -0.5 -0.5 0.5 0 0 0 0] But is testing for gender as a covariate same as testing group*gender interaction? I do not feel so. Hence requesting you all to throw some clarity on this. If this is not the way to study gender as a covariate how else should the contrast matrix be written? And regarding age should it be four 0.5s for the last 4 columns of the matrix if we want to study age as a covariate? Kindly let know. Finally I want a contrast matrix that studies the group differences in cortical thickness covarying for the effect of age and gender. Kindly help me. Thanks, Dr. Rakshathi Basavaraju (MD Psychiatry) Postdoctoral Research Scientist Taub Institute Columbia University Irving Medical Centre 622 West, 168th Street, New York - 10032 E-Mail: rb3419(a)cumc.columbia.edu<mailto:rb3419@cumc.columbia.edu> http://www.wellcomedbt.org/fellowsprofile/dr-rakshathi-basavaraju-288

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I have a question for "matlabruntime"
by Gwang-Won Kim 24 Jun '19

24 Jun '19

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(no subject)
by fsbuild 23 Jun '19

23 Jun '19

External Email - Use Caution Hello John, You might be able to tell from the log what directory recon-all was cd'd into when the creation of the soft link failed.  You could try to cd there as your userid (which I assume you used to run recon-all), and see if you can manually create any soft link there.  if you cannot do so, there could be a problem with the directory permissions.  The uersid running recon-all should have permission to read, write, and execute on subdirectories which typically means the permission on them is set to be 755. While do not officially support cuda, I would first check to see you have the cuda libraries installed on you system.  You could do a search under /usr to see if you have it, e.g. $ sudo find /usr -name "libcudart*" - or with the package tools, look to see if any nvidia or cuda packages are installed,  e.g., $ rpm -qa | grep -i nvid $ rpm -qa | grep -i cuda If you don't find a libcudart.so.5 installed, then I think you will need to install rev 7.5 of the cuda tools on your system as that should be the version with libcudart.so.5 - R. John Absher June 22, 2019 at 22:28 External Email - Use Caution Hi, I am testing a new installation of freesurfer. Two errors occurred, and I'm hoping someone can help me troubleshoot: First, recon-all exits with error indicating that it is unable to create a symbolic link: [GHS\026278@vmcntdsktp10 fs_sample1]$ tail /neuro_images_isilon/026278/fs_sample1/sample001/scripts/recon-all.log ICI = 216.7, FI = 1989.1, variation=32373.324 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux vmcntdsktp10 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sample001 exited with ERRORS at Sat Jun 22 17:10:41 EDT 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting The error occurs in CentOS 7 running on a virtual machine environment, with the latest stable freesurfer release, 6.0. The recon-all process was being run on the sample_001.mgz file to test the installation, and ran for about 7 hours. Second, when I tried to use the -use-gpu flag, the process seems to be missing a library: [GHS\026278@vmcntdsktp10 fs_sample1]$ recon-all -subject sample001 -i ./sample-001.mgz -use-gpu -all Testing for CUDA device: /usr/local/freesurfer/bin/mri_em_register_cuda: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory Linux vmcntdsktp10 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sample001 exited with ERRORS at Sat Jun 22 10:05:12 EDT 2019 For more details, see the log file To report a problem, see http://surfer.nmr.mgh..harvard.edu/fswiki/BugReporting [GHS\026278@vmcntdsktp10 fs_sample1]$ Can you suggest workarounds for one or both of these errors? Thanks, John Warm regards, Please, note my new email address, john.absher(a)prismahealth.org John R. Absher, MD, FAAN Division of Neurology, Department of Medicine Prisma Health-Upstate 200 Patewood Drive, Suite 350B City, SC 29615 864-454-4500 (office) 864-350-6655 (mobile) 864-454-4505 (fax) Inspire health. Serve with compassion. Be the difference. ---------------------------------------------------------------------- CONFIDENTIALITY NOTICE This message is intended only for the use of 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, you are hereby notified that any dissemination, distribution, or copying of this communication is strictly prohibited by law. If you have received this communication in error, please notify me immediately. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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question for preprocessing
by ping cao 23 Jun '19

23 Jun '19

External Email - Use Caution Dear expert， Thank you for reading! I want to do these four pre-processing steps: 1. Re-sampling each MR image to 256*256*256; 2. Using the N3 algorithm for intensity inhomogeneity correction; 3. Skull stripping; 4. Removing the cerebellum. Does " *recon-all"* do all the above 4 steps automatically? If so, which file is just finished with these four steps? If not, how can I do these steps? Your help is greatly appreciated. Best, ping

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