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30070 discussions

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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Recon-all w/ Hammersmith atlas
by Ryan Flores 24 Apr '18

24 Apr '18

Hi Freesurfer Developers, Our group is hoping to obtain the cortical thickness, surface area, and volume for various cortical regions (as well as some subcortical volumes); however, we would like these values to be outputted with respect to the regions delineated in the Hammersmith atlas. This atlas is available for free online (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-…) and I’ve included a screenshot to show you what files are included in the download. Based on this information, what is the best and/or most straight forward to move forward? Thank you for your time. I look forward to hearing from you. 1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 2. Platform: macOS High Sierra (Version 10.13.1) Best, Ryan -- Ryan Flores Clinical Research Coordinator

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resting state motion censoring
by Adam Martersteck 24 Apr '18

24 Apr '18

Hi Freesurer experts, I’m looking to censor (drop volumes) from my resting state fMRI time series that violate a predetermined motion and signal threshold (FD and DVARS). I've already determined which volumes violate X and Y criteria. Is there a way to to tell FS to "ignore" these time points in the analysis such as in preproc-sess or mkanalysis-sess? If there is not and if I were to drop the volumes directly from the 4D file before starting any pre-processing and analysis – would that be a problem for finding and regressing the auto-correlation in the time series? Thanks! Adam

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Re: [Freesurfer] Non-rigid registration approaches
by Hedyeh Javaheri 24 Apr '18

24 Apr '18

External Email - Use Caution 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 ------------------------------------------------------------ ----------------------------------------------------------------- Date: Tue, 17 Apr 2018 11:49:04 -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: <763da2ef-359a-9f44-9b54-1f96acb3b2ef(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Not really. Are you trying to account for B0 distortion in the DTI? If you have a B0 map, you can pass that to bbregsiter and mri_vol2vol to account for it On 4/16/18 10:29 AM, Hedyeh Javaheri wrote: > Hello all, > > I am performing DTI analysis and wanted to know if Freesurfer has a > tool for non-rigid registration. > I performed recon-all and dt_recon on my subject and then used the > register.dat file that was generated by dt_recon to convert the > dt_recon output files back into the space of my orig.nii file from the > recon-all output. Now I need to register the files in the orig.nii > space back onto the T1 MRI that is in native space. > > I have tried using? mri_vol2vol to get the files in the orig.nii > (recon-all) space into the T1 native space without using a > registration file (I used --regheader) and now the registration matrix > of my file is the same as the native space, but when I use rview to > visualize the registration there are flaws. I've also tried this > co-registration using tkregister2 to create a registration file called > register.native.dat, and then used mri_vol2vol with > register.native.dat; and the results were the same as when I used > mri_vol2vol with --regheader. > > Is there a tool to do actual manual registration in Freesurfer? Using > tkregister2 I cannot perform localized changes; and the global changes > it is capable of do not improve on the coregistration. > > Here is a breakdown of what I have done: > > subject in Native space to Freesurfer conformed space using recon-all, > output: orig.nii > subject in Native space to other Freesurfer space using dt_recon, > output: lowb.nii and register.dat > From the other Freesufer space to Freesurfer conformed space using > register.dat, output: lowb2orig.nii > attempting to convert from Freesurfer conformed space to Native space: > ? ? ? ? ? ? ? ? ? using mri_vol2vol and --regheader --> poor registration > ? ? ? ? ? ? ? ? ? using tkregister2 to make register.native.dat, then > mri_vol2vol and ?register.native.dat --> poor registration > > I am running Freesurfer version 6 on Windows. > > Thanks in advance! > -Hedyeh Javaheri

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