Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30083 discussions

Custom Segmentation of the Cortex usable with mri_compute_volume_fractions
by Pfannmoeller, Joerg Peter 10 Sep '19

10 Sep '19

Hello, I would like to generate a custom segmentation of the cortex. That segmentation should be restricted to a certain labeled region (e.g. a Brodmann Area). If possible I would also like to restrict the region to the lower half or upper half of the cortex. Let's call these new segmentations sub-segmentations. I would like to use mri_compute_volume_fractions with this segmentation to compute the volume fractions of the voxels in a scan that overlap with these new sub-segmentations of the cortex. Are there tools for this purpose in FreeSurfer? Best Joerg

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question on GLM
by Barletta, Valeria 10 Sep '19

10 Sep '19

Good afternoon! I have a question on the Freesurfer GLM. The command: mri_glmfit-sim --glmdir ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_cme} --cache 1.3 neg is giving me blue clusters (see attached picture). Do blue clusters mean that my variable y is LOWER in the FIRST or the SECOND group listed in the FSGD file? Thanks, Valeria

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Convert nifti atlas into .annot file
by Dev vasu 10 Sep '19

10 Sep '19

External Email - Use Caution Dear all, How can i create .annot files for both left and right hemisphere from nifti atlases http://www.gin.cnrs.fr/en/tools/aal/ are there any specific guidelines or commands for surface based parcellation ? Thanks Vasudev

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eTIV and brainmask mismatch on Philips data
by Agnieszka Sabisz 10 Sep '19

10 Sep '19

External Email - Use Caution Hi all! We are running FS v.6.0. on a supercomputer operating on Linux. We have two sets of data - one from 1.5T Aera Siemens, second from 3.0T Achieva TX Philips. The T1 images on both scanners have comparable CNR, with an isotropic resolution of 1mm3 each. The recon-all finished with no errors, but in approximately half of the Philips data there is a significant (up to 40%) difference between the brain mask volume and eTIV (no such problem on Siemens). We inspected the Talairach registration (as is pointed that eTIV is calculated upon it) in the mismatched data with: tkregister2 --mgz --s <subject> --fstal --surf orig and in the corrupted data the brain mask and the WM-GM borders align in terms of placement but are of a wrong scale (proportionate to the "brainmask-to-eTIV" difference). What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Attached you will find example tkregister2 output screenshots. Best regards, Agnieszka Sabisz

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[FREESURFER] longitudinal processing base_tmps does not exist error
by Lee, Seonjoo 10 Sep '19

10 Sep '19

External Email - Use Caution Dear Freesurfer, Could you help me to resolve this error? I looked up the previous postings, but the recommendation (copying files in the same folder etc.) did not help. Thank you. $ recon-all -base template -tp 002_S_0295_S32678 -tp 002_S_0295_S567612 -sd $SUBJECTS_DIR Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /Users/seonjoolee/ADNI_long/tmp Actual FREESURFER_HOME /Applications/freesurfer Darwin Seonjoos-iMac.nyspi.local 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 Started at Wed Aug 7 10:24:55 EDT 2019 Ended at Wed Aug 7 10:24:56 EDT 2019 #@#%# recon-all-run-time-hours 0.000 recon-all -s template finished without error at Wed Aug 7 10:24:56 EDT 2019 done $ recon-all -long 002_S_0295_S32678 template -all ERROR: file /Users/ll/ADNI_long/tmp/template/base-tps does not exist!

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Correcting defect problem after checking skull stripped and editing wm.mgz
by Jiun Wei Chen 10 Sep '19

10 Sep '19

External Email - Use Caution Dear freesurfer experts, When executing recon-all in two subjects with brain lesions, the recon-all process stopped at CORRECTING DEFECT 13 (vertices=49319, convex hull=12973, v0=65403) and CORRECTING DEFECT 6 (vertices=23529, convex hull=6740, v0=16029), respectively. After reading the relevant problem from freesufer mailing list, I had checked the skull and cerebellum not attached to the surface, two hemispheres are separated using freeview. In addition, I also load the brain.mgz, wm.mgz, ?h.orig.nofix and ?h.inflated.nofix and separately overlap the ?h.defect_label onto ?h.orig.nofix , ?h.inflated.nofix to edit wm.mgz to solve this problem. However, after editing wm.mgz in two subjects, the recon-all process still stopped at CORRECTING DEFECT 0 (vertices=32853, convex hull=7926) and CORRECTING DEFECT 6 (vertices=16533, convex hull= 4510) , respectively. Although I try to erase the non-white matter and label voxels as white matter as much as possible, there are too many voxels I think I need to label, which may cause the failure. I can't figure out how to continue to solve this problem. I use freesurfer version 6.0.0. I really appreciate your help. Thanks a lot. Best regards, Jiun-Wei

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Re: [Freesurfer] Issue downloading FS-FAST fMRI tutorial data {Disarmed}
by fsbuild 09 Sep '19

09 Sep '19

External Email - Use Caution OK, give it another try. - R. I have the same issue for the following command:wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gzIf you could add that file too, that would be great.RamiOn Mon, Sep 9, 2019 at 4:04 PM fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        There should be a file there now, so please try it again.- robOn Sep 9, 2019, at 14:26, Rami Hamati <rhama036(a)uottawa.ca> wrote:        External Email - Use Caution        Hello there,When attempting to get the analysed functional data using the below command:wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gzI get the following OUTPUT error:--2019-09-09 14:21:20--  ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz           => ‘fsfast-functional.tar.gz’Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)... 132.183.240.105Connecting to surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)|132.183.240.105|:21... connected.Logging in as anonymous ... Logged in!==> SYST ... done.    ==> PWD ... done..==> TYPE I ... done.  ==> CWD (1) /pub/data ... done..==> SIZE fsfast-functional.tar.gz ... done.==> PASV ... done.    ==> RETR fsfast-functional.tar.gz ... No such file ‘fsfast-functional.tar.gz’.Could you please advise.Thank you,Rami_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Rami Hamati, MSc. Nsc (Candidate)Royal's Institute of Mental Health ResearchMood Disorders Research Unit1145 Carling Ave, Ottawa, ON K1Z 7K4T: 613-722-6521 ext. 6838rhama036@uottawa.ca_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Issue downloading FS-FAST fMRI tutorial data
by fsbuild 09 Sep '19

09 Sep '19

External Email - Use Caution There should be a file there now, so please try it again. - rob On Sep 9, 2019, at 14:26, Rami Hamati <rhama036(a)uottawa.ca> wrote:        External Email - Use Caution        Hello there,When attempting to get the analysed functional data using the below command:wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gzI get the following OUTPUT error:--2019-09-09 14:21:20--  ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz           => ‘fsfast-functional.tar.gz’Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)... 132.183.240.105Connecting to surfer.nmr.mgh..harvard.edu (surfer.nmr.mgh.harvard.edu)|132.183.240.105|:21... connected.Logging in as anonymous ... Logged in!==> SYST ... done.    ==> PWD ... done.==> TYPE I ... done.  ==> CWD (1) /pub/data ... done.==> SIZE fsfast-functional.tar.gz ... done.==> PASV ... done.    ==> RETR fsfast-functional.tar.gz ... No such file ‘fsfast-functional.tar.gz’.Could you please advise.Thank you,Rami_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Extracting contrast data from mri_glmfit to graph
by cody samth 09 Sep '19

09 Sep '19

External Email - Use Caution Hello, I have a question regarding how to graph results that came from a vertex wise analysis using the command mri_glmfit and mri_glmfit-sim. I was interested in investigating an interaction effect between groups and my variable of interest (continuous) while co-varying for three nuisance variables. After running mri_glmfit and mri_glmfit-sim to correct for multiple comparisons. I visualized the results and found significant clusters. I'm interested in graphing these results. Based on archived questions to this mailing list the individual values for each cluster can be found within the ocn.dat file and the cluster information can be found in the summary file. My analysis looked at volume, thickness and surface area. Since mean volume and area is difficult to interpret I want to convert the values to a total measure. It has been suggested in the past this can be done by multiplying each individuals values within the ocn.dat file by the number of vertices the cluster has. However, from my understanding this could be done by altering the mri_segstats command (that mri_glmfit-sim automatically runs) to include the --accumulate option. When I do these methods to convert mean area and volume to total area and volume the results are different. My first question is 1) Shouldn't these values be identical? The values from multiplying mean volume by number of vertices are roughly around 3500. Whereas using the --accumulate in mri_segstats are around 2500. What could be causing this discrepancy? 2) If my cluster has a size of 1500 mm^2 (in a model for area) does it make sense that every individual's values after extraction and conversion to total area are larger than the cluster size? 3) ocn.dat files are the input values meaning they're raw and would need to be corrected in a statistically (in a similar way that I modeled it in freesurfer) before graphing right?

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freesurfer 6.0 hires fix
by Aaron Tanenbaum 09 Sep '19

09 Sep '19

External Email - Use Caution I noticed that you guys released a fix to improve the -hires option. I have been processing some of our data using the hires flag. if i use this fix do i need to run recon-all from the beginning or can I run over the old folders?

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