Freesurfer June 2018

freesurfer@nmr.mgh.harvard.edu

105 participants
154 discussions

Grad-unwarp
by Maryam Abaei 11 Jun '18

11 Jun '18

External Email - Use Caution Dear Team, I am trying to use gradunwarp function but I can't go furher than first command. I can run perl gradient_unwarp_converter.pl and there is no error at all ( and it says writing alpha/beta sections....) but doesn't create the coef files that I need in sext step. I was wondering if you know how I can fix this. Best wishes, Maryam

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Extracting the centroids from Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz atlas
by zuxfoucault Wong 11 Jun '18

11 Jun '18

External Email - Use Caution Dear Freesurfer experts, I intended to extract centroid of the atlas "Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz" According to the post: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-May/057046.html I used the command as: """ source_img_fname=${FREESURFER_HOME}"/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz" color_lut=${FREESURFER_HOME}"/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_ColorLUT.txt" mri_segcentroids --i ${source_img_fname} --o ./Buckner2011_17Networks_centroid.txt --ctab ${color_lut} """ Am I use it the right way? Also, I am wondering how to transform the volumetric 17Networks centroids to embed to surface-based fsaverage network centroids (scripts as https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-February/056056.…) ? Thank you for your time! Best, Foucault

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I ran the linear mixed model matlab code on DTI-data (FA) from tbss (700 subjects and ca. 130 000 voxels) but converges only on 30 %
by Knut J Bjuland 11 Jun '18

11 Jun '18

External Email - Use Caution Dear FreeSurfer experts, I ran the linear mixed model matlab code on DTI-data (FA) from tbss (700 subjects and ca. 130 000 voxels). I adapted the code a little bit to accommodate the data format. I have a longitudinal design with 3 time points and two groups, the model is intercept (random factor) + group (patients, controls) + centered age + sex + a continuous clinical variable. Centered age = age - mean age for all observations (across all subjects, groups, and time points). The scripts run without crashing but lme_fit_FS.m converges in only ca. 30% of the voxels. lm_F produces F and p-values that I can use. However, I'm uncertain what to make of the messages about "Algorithm does not converge after 50 iterations!!!" Does that invalidate the analyses? Or can I use the resulting pvals even where lme_fit_FS did not converge? Also, I'm not used to such a high rate of non-convergence. Any idea what may be going wrong? The FA-data looks fine (between 0 and 1; mean = 0.49; SD = 0.15). Thank you! Knut Jørgen Bjuland

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Re: [Freesurfer] get thickness and gray volume
by Bruce Fischl 10 Jun '18

10 Jun '18

also in the stats dir (check aseg.stats) cheers Bruce On Mon, 11 Jun 2018, charujing123 wrote: > > External Email - Use Caution > > Hi Bruce and FS experts, > I have resolved that question. another one is that how to get subcortical gray volume or thickness? > Thanks. > Best. > Rujing > > 2018-06-11 > > ____________________________________________________________________________________________________ > charujing123 > > ____________________________________________________________________________________________________ > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > 发送时间：2018-06-10 23:28 > 主题：Re: get thickness and gray volume > 收件人："charujing123"<charujing123(a)163.com> > 抄送："freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > Hi Rujing > > have you looked the the stats file in each subject's stats dir? They > should contain these measures in text format. > > cheers > Bruce > On Sun, 10 Jun 2018, > charujing123 wrote: > > > > > External Email - Use Caution > > > > Hi FS experts and Bruce > > I have done the recon-all, and -qcache -measure thickness. Then I want to get thickness and gray > > > volume for each fsaverage atlas regions, and it would be better in a txt format. > > Thanks. > > Looking forward any kindhearted reply. > > Best. > > Rujing > > > > 2018-06-10 > > > > _________________________________________________________________________________________________ > ___ > > charujing123 > > > > > > > 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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Unusual hires T1 specs
by Juranek, Jenifer 10 Jun '18

10 Jun '18

External Email - Use Caution I offered to help a colleague with some Freesurfer analyses, but when I looked at the data they were processing, I found: 1) highly anisotropic voxdims 2) sub-mm in-plane resolution Data were acquired on a 3T Siemens Tim Trio. I don't think they were trying to deviate from the recommended 1x1x1mm specs, but somehow it looks like they did since the 001.mgz file does not conform to the FS standard. Output for mri_info on their 001.mgz file is listed below. They did not keep the file converted by mri_convert (nii or dicom) in their FS_sub directory, so I'm limited to the 001.mgz. I'm running FSv6 in my lab, is the hires flag appropriate in this situation? Any suggestions? Many Thanks, Jenifer [orig]$ mri_info 001.mgz Volume information for 001.mgz type: MGH dimensions: 448 x 512 x 192 voxel sizes: 0.478516, 0.478516, 1.000000 type: SHORT (4) fov: 245.000 dof: 0 xstart: -107.2, xend: 107.2 ystart: -122.5, yend: 122.5 zstart: -96.0, zend: 96.0

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Re: [Freesurfer] get thickness and gray volume
by Bruce Fischl 10 Jun '18

10 Jun '18

Hi Rujing have you looked the the stats file in each subject's stats dir? They should contain these measures in text format. cheers Bruce On Sun, 10 Jun 2018, charujing123 wrote: > > External Email - Use Caution > > Hi FS experts and Bruce > I have done the recon-all, and -qcache -measure thickness. Then I want to get thickness and gray > volume for each fsaverage atlas regions, and it would be better in a txt format. > Thanks. > Looking forward any kindhearted reply. > Best. > Rujing > > 2018-06-10 > > ____________________________________________________________________________________________________ > charujing123 > >

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recon-all -s subid exited with ERRORS
by Lee, Seonjoo 10 Jun '18

10 Jun '18

External Email - Use Caution Hi Bruce, recon-all did not run, and I could not figure out the problem. Do you have any clue what could be? The log file does not tell anything… The command was the most simplest one (using only t1). If you need more information to figure out the cause of this error, please let me know. Thank you. -Seonjoo ==== #@# MotionCor Sat Jun 9 21:04:46 EDT 2018 Found 1 runs subject/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. \n cp subject/mri/orig/001.mgz subject/mri/rawavg.mgz \n subject \n mri_convert subject/mri/rawavg.mgz subject/mri/orig.mgz --conform \n mri_convert.bin subject/mri/rawavg.mgz subject/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from subject/mri/rawavg.mgz... TR=6.81, TE=3.16, TI=0.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to subject/mri/orig.mgz... Darwin Seonjoos-iMac.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 recon-all -s subid exited with ERRORS at Sat Jun 9 21:04:51 EDT 2018

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Prospective motion correction sequences
by Backhausen, Lea 08 Jun '18

08 Jun '18

External Email - Use Caution Dear FreeSurer experts, has anyone of you ever used prospective motion correction techniques like PROMO or BLADE/PROPELLER? We are planning a new study with children and adolescents with obsessive-compulsive disorder and thought about implementing special motion correction sequences for the structural data as we are very aware of potential motion artifacts in pediatric clinical samples like this one. Still we are not sure whether special sequences like these could potentially change the raw data in any way that may corrupt FreeSurfer reconstruction. I read a lot of positive reviews about PROMO, would you recommend it? Thank you for your input! Best Lea ------------------------------ Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>

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ERROR running mkcontrast, ERROR: cannot find matlab. Is it in your path?
by 高寒 08 Jun '18

08 Jun '18

External Email - Use Caution 高寒已与你共享 OneDrive 文件。若要查看，请单击下面的链接。 <https://1drv.ms/u/s!AuDaBb5FCQKSglY7fUCYI2K7qRCu> [https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]<https://1drv.ms/u/s!AuDaBb5FCQKSglY7fUCYI2K7qRCu> 终端存储的输出<https://1drv.ms/u/s!AuDaBb5FCQKSglY7fUCYI2K7qRCu> Hello FreeSurfer Developers, I am running FS-FAST on my mac. My freesurfer version is freesurfer-i386-apple-darwin11.4.2-stable6-20170119. My MAC version is macOS High Sierra 10.13.4 (17E202). I downloaded Matlbab Runtime on this site: http://www.freesurfer.net/fswiki/MatlabRuntime as constructed. When I run this command: { mkcontrast-sess -analysis my-language.sm05.lh -contrast language-v-base -a 1 }, I kept getting this error. ERROR: cannot find matlab. Is it in your path? ERROR running mkcontrast Then I downloaded Matlab runtime R2014a (8.3). I still got the same error as above. Then I downloaded Matlab runtime R2018a (9.4). Still the same error. I assume I should download a certain version of Matlab Runtime in order to run FS-FAST on freesurfer-i386-apple-darwin11.4.2-stable6-20170119 on my macOS High Sierra 10.13.4 (17E202). Could you help me? Thank you.

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-qcache in recon-all commnd
by Alexopoulos, Dimitrios 07 Jun '18

07 Jun '18

Is it recommended to use the -qcache flag in the basic recon-all -all command? What does it do and what are the advantage of using it? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Freesurfer June 2018