Freesurfer April 2018

freesurfer@nmr.mgh.harvard.edu

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177 discussions

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Using mprage flag.
by Aaron Tanenbaum 26 Apr '18

26 Apr '18

External Email - Use Caution Hello FreeSurfers When should I use the MPRAGE flag for recon-all? Aaron Tanenbaum

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mri_compute_volume_fractions
by Srinivasan, Dhivya 26 Apr '18

26 Apr '18

External Email - Use Caution Hi, I would like to get CSF/GM/WM segmentations from aseg.mgz or in other words from labeled brain. Can I do that with mri_compute_volume_fractions ? Also, I am not sure about the parameters to supply, <reg file> and <output stem>? Could Someone point me to some documentation on how should use this function to get the segmentations ? Thanks, Dhivya

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aparcstats2table for white surface total area
by Sian Emma Davies 26 Apr '18

26 Apr '18

External Email - Use Caution Hello, Forgive me, I'm new to FreeSurfer. I wish to collate values of white surface total area from all my subjects into a single table, so that I can control for this in my analyses. I understand this value is in the aparc.stats files for each participant and hemisphere, so I have tried: aparcstats2table -subjectfile sublist -hemi lh -meas WhiteSurfArea -tablefile aparc_stats_lh.wsa.table but WhiteSurfArea isn't an option for -meas. Please let me know if you can help, Many thanks, Emma Davies PhD Student Department of Psychiatry University of Cambridge Douglas House 18b Trumpington Road Cambridge CB2 8AH

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recon-all with T1 and T2 images
by Heidi Lindroth 26 Apr '18

26 Apr '18

External Email - Use Caution Hello, I have processed the majority of my T1 images using the general recon-all command. After reviewing segmentation, a number of images have the pial surface included in the gray matter. I re-ran an image with the recon-all command combining the T1 and T2 images and it greatly reduced the segmentation errors. Going forward, are there quality differences between those images processed with only recon-all versus those processed with recon-all T1 & T2? Can I still combine images processed with T1 only and those with T1 & T2 in the same analysis? Or, do I need to rerun all scans with the recon-all T1 & T2 command? Thank you, Heidi Lindroth BSN RN PhD Candidate | School of Nursing Program Assistant | School of Medicine and Public Health, Department of Anesthesiology Predoctoral Fellow | Veterans Administration (Madison WI) University of Wisconsin-Madison 701 Highland Avenue, Madison WI 53705 608-219-4294 | hlindroth(a)wisc.edu<mailto:hlindroth@wisc.edu>

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Re: [Freesurfer] Non-rigid registration approaches
by Hedyeh Javaheri 25 Apr '18

25 Apr '18

External Email - Use Caution Hi Douglas, I applied a non-rigid registration to my nifti files using another software (IRTK) and then tried to run dt_recon in Freesurfer. Dt_recon is failing during Fitting Tensors and the error message it is displaying is "ERROR: DTIstructFromBFiles(): dimension mismatch" the error message goes on to say that my bvecs file has 99 rows while my bvals file has 11 rows. I've looked at my bvecs and bvals files: the bvecs has 33 rows and 3 columns, and the bvals has 33 rows and 1 column. Can you tell me what the problem is? Is there a way to get past this error? -Hedyeh Date: Tue, 24 Apr 2018 13:20:20 -0400 From: Douglas Greve <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Non-rigid registration approaches To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <52506cd6-286b-21a0-859a-1cda85557bad(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Sorry, I don' know what to tell you. On 4/21/18 5:34 PM, Hedyeh Javaheri wrote: > > > Thanks for your reply Douglas, > > I am trying co-register the Diffusion data onto the original > structural MRIs. I have tried bbregister and mri_vol2vol but the > results are not great. I realized that the diffusion data have a lot > of distortions, so the rigid and/or affine co-registration is not > sufficient. Do you recommend performing a non-rigid registration in > this case? If you do, do you know of any ways to do that within > Freesurfer? > > > Thanks > > -Hedyeh

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Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found
by Nillo, Ryan Michael R 25 Apr '18

25 Apr '18

External Email - Use Caution Hello FreeSurfer users, I am trying to run hippocampal subfield segmentation on our subjects on FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an error relatively early: /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin//kvlAutoCrop: line 3: kvlAutoCrop.bin: command not found When I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin, kvlAutoCrop.bin was located there, as expected. When I tried to run the step manually, it produced the correct output, but the next step gave me the similar error: command not found. I looked into /netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin and saw all the other binaries were there, as well. The binaries are correctly exported on my PATH. I also made sure to download the Matlab compiler runtime and made sure they were on my PATH. I am running freesurfer on a Linux machine with the RedHat 7.5 OS.Any help is greatly appreciated. Thanks, Ryan

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Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found
by Nillo, Ryan Michael R 25 Apr '18

25 Apr '18

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Arcuate fasciculus seed regions in MNI space
by Juergen Haenggi 25 Apr '18

25 Apr '18

External Email - Use Caution Dear tractography experts does anyone have the arcuate fasciculus seed regions in MNI space and is willing to share these seeds with us? we are also interested in MNI space seed regions of the different parts of the SLF (according work done by Catani and colleagues). Thanks in advance Regards Jürgen ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This email (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this email in error) please notify the sender immediately and destroy this email. Any unauthorised copying, disclosure or distribution of the material in this email is strictly forbidden. -----------------------------------------------------------------------------------------------------

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Segmentation issue with FS6
by Barlow, Cody 24 Apr '18

24 Apr '18

External Email - Use Caution Hi FreeSurfer Experts, After running my subject through FS6 autorecon3 and QCing the data, I noticed that FS6 is outlining white matter as grey matter and then bumping out the grey matter segmentation accordingly. I have tried using different watershed preflood heights during various skull strips with no success as well as using the flag gcut. I'm thinking the issue has to do with atrophy due to my subject population, dementia patients, or poor contrast between GM and WM during image acquisition. Is there a flag or tkmedit tool I can use to help solve this problem. I have attached an image showing the issue. Thanks for the help, Cody

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Calculation of surface area
by Zohar Berman 24 Apr '18

24 Apr '18

External Email - Use Caution Dear FreeSurfer experts, Can one use the volume and cortical thickness of a region to calculate the surface area of this region? Thanks a lot in advance! Best, Zoi

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Freesurfer April 2018