Freesurfer

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30099 discussions

Specify Brain Region as Dependent Variable
by Chris Wertz 24 Jun '14

24 Jun '14

Hi Freesurfer experts, Is it possible to change the dependent variable of a whole hemisphere's thickness to a specific brain region's thickness? For example I wish to test one of my independent variables with right hemisphere superior parietal region's thickness as opposed to the whole right hemisphere's thickness. Thanks, Chris

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A comparison between atlases
by Dorian P. 24 Jun '14

24 Jun '14

Dear Freesurfer followers/developers, I am doing a study involving temporal lobes and the parcellations from Desikan and Destrieux atlases have very different results. I like the full gyrus parcellation of Desikan but the temporal pole is very small and limited, while in Destriux the temporal pole is bigger and more appropriate to be studied separately. My question is: can I combine parcellations from these atlases? I.e., if I subtract the temporal pole from Destriuex from the map of Desikan, will I take off all the anterior temporal pole gray matter, or is there any potential mismatch between parcellations so there will remain voxels in the anterior temporal lobe? Thank you. P.s. One less important question I have is this. I have noticed that wmparc.mgz is the same as aparc+aseg.mgz with the addition of white matter parcels. For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this file have also the WM parcellation?

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Extracting mean diffusivity values from diffusion data in freesurfer 5.3
by Rotem Saar 24 Jun '14

24 Jun '14

Dear freesurfer experts, I'm using freesurfer 5.3 for extracting FA and MD values for each region from the *aseg file for each subject. While I get validated FA values (I validated them with you, the literature and some other software I used), I have a problem getting reasonable MD values. This is the script I'm using for extracting the MD values: 1) dt_recon --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/I160.dcm --s Anatomy0981 --o /usr/local/freesurfer/subjects/Anatomy0981/DTI --b /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec 2) mri_label2vol --seg /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --temp /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --reg /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --o /usr/local/freesurfer/subjects/Anatomy0981/DTI/forMD.mgz 3) mri_segstats --seg-erode 1 --seg /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/forMD.mgz --sum /usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked It writes *.txt files similar to the ones of the FA (and also the volumetric analysis) which is good, but - 1) I can't understand the units (it is written "unknown"). can u tell me what do these units refer to ? 2) I can't understand why the units I get don't corresponds to the units in the literature (0-1). Is there a transformation I need to apply to these units in order to get the values we all see in the literature (MD values ranges between 0 to 1 in the papers I read). 3) I am concerned about the differences in the values both between and within subjects. For example, see 3 different subjects and their MD values for the corpus-callosum: subject 1: 35 251 368 368.0 CC_Posterior 7.4783 7.9938 0.0000 16.0000 16.0000 36 252 110 110.0 CC_Mid_Posterior 56.7273 476.3758 0.0000 5002.0000 5002.0000 37 253 205 205.0 CC_Central 992.4537 1806.8883 0.0000 5002.0000 5002.0000 38 254 132 132.0 CC_Mid_Anterior 1664.2954 2328.8467 43.0000 5002.0000 4959.0000 39 255 277 277.0 CC_Anterior 1723.4620 1914.7883 0.0000 5002.0000 5002.0000 subject 2: 36 251 328 328.0 CC_Posterior 0.0000 0.0000 0.0000 0.0000 0.0000 37 252 78 78.0 CC_Mid_Posterior 43.9744 226.6371 0.0000 2000.0000 2000.0000 38 253 100 100.0 CC_Central 203.0800 779.8602 0.0000 5001.0000 5001.0000 39 254 83 83.0 CC_Mid_Anterior 264.5783 364.1581 0.0000 1002.0000 1002.0000 40 255 321 321.0 CC_Anterior 985.8879 720.5300 0.0000 3028.0000 3028.0000 subject 3: 35 251 424 424.0 CC_Posterior 20.6840 6.6236 10.0000 60.0000 50.0000 36 252 160 160.0 CC_Mid_Posterior 143.4312 780.4187 0.0000 5001.0000 5001.0000 37 253 202 202.0 CC_Central 538.0248 1143.9441 0.0000 5001.0000 5001.0000 38 254 179 179.0 CC_Mid_Anterior 496.5140 623.4088 0.0000 2023.0000 2023.0000 39 255 361 361.0 CC_Anterior 211.6094 539.0007 0.0000 2028.0000 2028.0000 the values are really different both within the CC parts of the same subject (does this make any sense ??) and also between subjects... We ruled out a problem in the gradient matrix (both with you and because the FA values corresponds to reasonable values both from the literature and other software we use). Can u please advise on how can we solve this issue ? We are in the middle of submission of a very novel study and were required to show addition analysis of the MD values - this is why this is so impotent to us. Attached please find the full *.txt files I got. Thanks for your help. Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel

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mri_ca_register error
by Liesel-Ann Meusel 24 Jun '14

24 Jun '14

Hi, I am running recon-all and I am getting the following error during the mri_ca_register step (full log file is attached). Please let me know what I need to do to fix it. Thank you, Liesel writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 4 hours, 17 minutes and 32 seconds. ERROR: mri_ca_register with non-zero status 1 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Sun Jun 1 22:03:47 EDT 2014 /home/lmeusel/101_TEST/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse ERROR: mri_ca_register with non-zero status 0 Linux gateway.neuroinfo.rri 2.6.32-279.9.1.el6.x86_64 #1 SMP Tue Sep 25 21:43:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 101_TEST exited with ERRORS at Sun Jun 1 22:04:52 EDT 2014 -- Liesel-Ann Meusel Postdoctoral Fellow Rm 722, Rotman Research Institute, Baycrest 3560 Bathurst St. Toronto ON M6A 2E1 416-785-2500 ext. 3507 lmeusel(a)research.baycrest.org

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Problem Visualization Hippocampal Subfields Freeview
by Joana Braga Pereira 24 Jun '14

24 Jun '14

Dear Freesurfers, I've been using freeview to visualize the hippocampal subfields segmentations in a group of subjects between 9 and 14 years of age. I observed that a strange black line is drawn around the subfields (please see attached figure) although the segmentation was carried out correctly. After exchanging some emails with an expert from the list, it seems that this problem is due to a visualization issue in freeview. Does anyone know how to solve it? I would like to take a snapshot of the subfields in freeview to make a figure. Thanks, Joana

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Re: [Freesurfer] free-surfer longitudinal Qdec table
by Martin Reuter 24 Jun '14

24 Jun '14

Hi Anna, whenever it says qdec-long the table is in qdec format (with a fsid-base as second column. It would then use the longitudinally processed results, which is what you want , both for lme and 2 stage model. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Anna Jonsson <ajonsson09(a)gmail.com> Date:06/09/2014 3:47 PM (GMT+01:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table Hi, sorry for more questions, but i have a few. When running the first step of the lme implemented tools, doing the command mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh (assembles your thickness data into a single lh.thickness.mgh file), am I correct that this just needs to be a "normal" cross-sectional qdec table that free surfer subsequently makes into long format by --qdec-long option? so the lnogitudinal qdec table is only used in the two stage modell? This too just uses the cross-sectionally derived scans? Im confused where the .long runs become used? thank you and kind wishes On Wed, Jun 4, 2014 at 5:01 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Anna, Fsid is the cross sectionall name without the .long. Best martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Anna Jonsson Date:06/04/2014 7:22 AM (GMT-05:00) To: Freesurfer support list Subject: [Freesurfer] free-surfer longitudinal Qdec table Hi, I would like to make my freesurfer longitudinal qdec table for the to use in the lme matlab tools. However, does the fsid need to refer to the longitidunally derived subject; eg XXX.long, or the cross-sectionally derived subject, eg XXX. Im not sure based on the specification online. Kind Regards Anna _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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mpr2mni305 failed, see transforms/talairach_avi.log
by Venkateswaran Rajagopalan 23 Jun '14

23 Jun '14

Hi All, I am getting the the following error when I run recon-all -subjid E368 -autorecon1 ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Here is what talairach_avi.log says /home/administrator/Desktop/freesurfer/subjects_dir/E368/mri /usr/local/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux Fri Jun 20 17:06:38 IST 2014 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 122.500; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Fri Jun 20 17:06:39 IST 2014 /usr/local/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:40 2014 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- $Id: gauss_4dfp.c,v 1.3 2009/05/15 21:43:46 nicks Exp $ Reading: talsrcimg.4dfp.img Writing: talsrcimg_g11.4dfp.img image dimensions 256 256 256 padded to 288 288 288 processing volume 1$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:46 2014 Writing: talsrcimg_g11.4dfp.hdr Writing: talsrcimg_g11.4dfp.ifh including: talsrcimg.4dfp.img.rec in talsrcimg_g11.4dfp.img.rec --------------------------------------------------------------------- imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355 --------------------------------------------------------------------- $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ imgreg_4dfp: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img read error /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=255 ERROR: mpr2mni305 execution aborted Any help will be greatly appreciated. Thanks Venkat

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Re: [Freesurfer] Why the result was not same for the same subject
by kangchengwang0808＠gmail.com 23 Jun '14

23 Jun '14

Dear Nick The recon-all.log for one time was in the attachment. Thank you Wang Kangcheng

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fMRI Image Acquisition and Analyses Course : October 16-18, 2014 (fwd)
by Bruce Fischl 23 Jun '14

23 Jun '14

FYI -- The Mind Research Network (MIND) is pleased to invite you to the fMRI Image Acquisition and Analyses Course held on October 16-18, 2014 on the campus of the University of New Mexico in Albuquerque, New Mexico. For more information and registration, see http://www.mrn.org/education-outreach/courses-and-events/ Special topics include the unique issues that multiband EPI (i.e., whole brain subsecond EPI) brings to fMRI analyses ***Email Kent A. Kiehl kkiehl(a)unm.edu or fMRIcourse(a)mrn.org with any questions. We hope to see you there. Thanks for your time, and have a great day!

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Infant atlas - finding control points
by Mark Plantz 23 Jun '14

23 Jun '14

Hello freesurfers, I am currently attempting to run recon-all on a set of infant brains with a non-default atlas. I was previously running into a problem where freesurfer was unable to find control points for the various labeled regions of the atlas. It appears as if the “wm_mean” of the atlas and subject are being set to 0. My thought is that the non-deafult atlas was resulting in some sort of null error where everything was just set to zero by default. This resulted in a completely blank “ctrl_points.mgz” and “norm.mgz” files. However, I recently noticed that the “aseg.auto_noCCseg.mgz” file looks like the atlas is actually mapping the various regions to the subject’s original T1 file. A screenshot of this file is attached to the e-mail. Does anyone have any ideas why the atlas would map correctly to the aseg file, but then fail to find any control points in those same regions? I attached the log file in case that would help. Thank you! - Mark

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