Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

ROI in FreeSurferColorLUT.txt
by stdp82＠virgilio.it 27 Apr '14

27 Apr '14

Hi list, I'm noting these regions in FreeSurferColorLUT.txt. How can I obtained structural information from them? 8001 Thalamus-Anterior 74 130 181 0 8002 Thalamus-Ventral-anterior 242 241 240 0 8003 Thalamus-Lateral-dorsal 206 65 78 0 8004 Thalamus-Lateral-posterior 120 21 133 0 8005 Thalamus-Ventral-lateral 195 61 246 0 8006 Thalamus-Ventral-posterior-medial 3 147 6 0 8007 Thalamus-Ventral-posterior-lateral 220 251 163 0 8008 Thalamus-intralaminar 232 146 33 0 8009 Thalamus-centromedian 4 114 14 0 8010 Thalamus-mediodorsal 121 184 220 0 8011 Thalamus-medial 235 11 175 0 8012 Thalamus-pulvinar 12 46 250 0 8013 Thalamus-lateral-geniculate 203 182 143 0 8014 Thalamus-medial-geniculate 42 204 167 0 and from 6010 Left-SLF1 236 16 231 06020 Right-SLF1 237 18 232 0 6030 Left-SLF3 236 13 227 0 6040 Right-SLF3 236 17 228 0 6050 Left-CST 1 255 1 0 6060 Right-CST 2 255 1 0 6070 Left-SLF2 236 14 230 0 6080 Right-SLF2 237 14 230 0Are the tracts different from tracts product by TRACULA? and can I use them with TRACULA outputs? Thanks, Stefano

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MNI <--> freesurfer coordinate conversion
by Kaveh Kohan 26 Apr '14

26 Apr '14

Hi Everyone, I was wondering if there is anyway to convert MNI coordinate to freesurfer coordinates? Let me explain a bit more: I have a set of points with their coordinates in the MNI atlas, I would like to find the closest ROI's (or better rank ROIs) with respect to their distance to those coordinates? Is there anyway to do this? Currently, I think I should find the center of the freesurfer ROIs (I don't know how!) and convert them to MNI coordinates and find the closest points? Is there any better way? Please advise, Regards, K

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Monte Carlo simulation - Longitudinal Pipeline
by Pedro Rosa 26 Apr '14

26 Apr '14

Dear list, I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline in a structural MRI dataset and I would like to use Monte Carlo as the method for correction for multiple comparisons. However, the longitudinal LME tutorial includes only FDR correction (lme_mass_FDR2). Is it possible to use Monte Carlo correction for longitudinal data? Can I input the outputs from MatLab (fstats = lme_mass_F(?h,CM): stats.F / pval / sgn / df) into mri_glmfit and then run Monte Carlo? If not, do you have any other suggestions of how I use Monte Carlo in longitudinal analyses? Thanks in advance, -- Pedro Rosa

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converting volume-based mask into surface-based fsaverage
by charujing123 26 Apr '14

26 Apr '14

Hi FS experts and users I created a rIPL mask by other tools and I want to make it surface-based mask. I ran this command: mri_vol2surf --hemi rh --reg register.dat --mov ./rIPL.nii.gz --o ./rIPL_afni.mgh --trgsubject fsaverage And it echo this output, that is to say, it cannot find the register.dat. I want to know where the file is : ============================= srcvol = ./rIPL.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume regio_read_register(): No such file or directory Could not open register.dat ==================== Thanks All the best Rujing Zha 2014-04-26 charujing123

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aparc+aseg.mgz recovery
by Daria Boratyn 25 Apr '14

25 Apr '14

Hi all, I accidentally damaged my aparc+aseg.mgz file. Is there any way to recover this without rerunning recon-all? Thanks so much! Daria

2 1

FreeSurfer on MacBook Pro
by Ebraheem, Ahmed 25 Apr '14

25 Apr '14

Dear Sir/Madame, I am trying to install and run Freesurfer on my new MacBook Pro 15.4" Retina 2880x1800 2.3GHZ Intel QC i7 Intel Iris Graphics 16GB RAM 512GB SSD ME294LL/A I am not sure why it's not running but I noticed that my OS is Mavericks and the download page says: Lion OX X 10.7 (64b Intel) or SnowLeopard OS X 10.6 (32b Intel) Could you please advise me on how to install and run Freesurfer on my machine? Thank you very much, Ahmed Ahmed Ebraheem, MBChB., M.Sc., Ph.D Concussion Fellow Neurology Division Toronto Western Hospital ahmed.ebraheem(a)uhn.ca This e-mail may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this e-mail may not be that of the organization.

1 0

recon-all subject -qcache in a different version of freesurfer?
by Yizhou Ma 25 Apr '14

25 Apr '14

Dear Freesurfer experts, I have processed my images and done analysis with cortical thickness using FS510. Now that I want to do vertex-wise analysis with surface area and volume, I learned that there is a bug in FS510 with this. ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019903.h… ) Before I go on to use recon-all subject -qcache in FS530 to generate vertex-wise surface area and volume maps, I want to make sure that this would not cause concerns about use of mixed versions of Freesurfer, or concerns about interpreting my cortical thickness and surface area/volume findings together. And if it does, what should I do? Thanks a lot, Cherry

2 4

Invalid license for recon-all
by Teodorescu, Roxana 25 Apr '14

25 Apr '14

Dear FreeSurfer experts, I have FreeSurfer installed on an Ubuntu system and I got the following error: ERROR: Invalid FreeSurfer license key found in license file /media/datas/study_tools/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment FreeSurfer was previously working on this computer without any errors. I have not been using it for a while and now I got this error. I got a new license and even though the .license file is updated and recon help works I still get the same error. Can you please help. Thank you. Roxana.

1 0

openmp/mkl support in tracula
by Satrajit Ghosh 25 Apr '14

25 Apr '14

hi a.y., is there any part of tracula that currently benefits from openmp or mkl availability? cheers, satra

2 1

convert volume-based mni152 space into fsaverage surface space(MNI305)
by charujing123 25 Apr '14

25 Apr '14

Hi FS experts and users, I created a mask volume, whose space is in MNI152 space. And I want to convert this volume into surface-based in fsaverage. How can I realize this? Thanks All the best. Rujing Zha 2014-04-22 charujing123

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