Freesurfer

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30088 discussions

Re: [Freesurfer] nuisance factors
by Georgina Angelopoulou 06 Nov '19

06 Nov '19

External Email - Use Caution Apologies for sending again, I would like to verify that you have received the email. Thank you in advance for you help, Georgina I am sorry, please let me rephrase. I want to compare patients vs controls in Surface area and grey matter volume. I have already checked age slope and it is not significant for either GMV or SA. However eTIV slope is significant in both cases (we do check for eTiv slope first as we did for age, right?) So in that case that we have two nuisance variables (age and eTiv), eTIV is significant but age isn't, how are we going to formulate the contrast? Would 1 -1 0 0 0 0 be correct? Thanks once again, Georgina

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Re: [Freesurfer] LME model contrast matrix (Diers, Kersten /DZNE)
by Liu Guodong 05 Nov '19

05 Nov '19

External Email - Use Caution Dear Kersten: The β1 and β2 in the tutorial model is the regressing coefficients for all the subjects not only for the control subjects because all the intercept are one. I wonder why the reference group is control group in this case? Thanks in advance. Best regards, Guodong > 在 2019年10月25日，上午12:00，freesurfer-request@nmr.mgh.harvard.edu 写道： > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. time point exlusion file exceed nframes (Lauri Tuominen) > 2. Re: time point exlusion file exceed nframes > (Greve, Douglas N.,Ph.D.) > 3. Re: Learning fsfast tutorial (Greve, Douglas N.,Ph.D.) > 4. Re: LME model contrast matrix (Diers, Kersten /DZNE) > 5. Re: Learning fsfast tutorial (Renew Andrade) > 6. Re: Learning dti processing tutorial (Renew Andrade) > 7. mri_cvs_register error while diffusion imaging processing > (Renew Andrade) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 23 Oct 2019 17:34:59 +0000 > From: Lauri Tuominen <ljtuom(a)utu.fi> > Subject: [Freesurfer] time point exlusion file exceed nframes > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <6506F69C-782A-4074-A898-17E58814EF58(a)utu.fi> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Dear Freesurfers, > I am running resting state analysis. I have TR 2.3, and 209 time points/frames, total length of the scan 483 seconds. I don?t drop any frames from the beginning ( nskip = 0 ). > > For one subject, the last two time points are motion outliers. So my tpef file includes numbers 478.4 and 480.7. When I run selxavg3-sess, I get the error time point exlusion file exceed nframes. > > I can?t figure out where the bug might be. So once again I would really appreciate your help! > Thanks > Lauri Tuominen > > > > > ------------------------------ > > Message: 2 > Date: Thu, 24 Oct 2019 03:28:21 +0000 > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] time point exlusion file exceed nframes > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <fee25413-e204-29d7-27c0-a69427052343(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Lauri, I think this comes down to whether you start counting from 0 > or 1. FSFAST starts from 0, so the time of? time point N is N*TR. The > maximum you can have is N=208, and so the max time would be 478.4. Your > 480.7 exceeds this limit. > doug > > On 10/23/2019 1:34 PM, Lauri Tuominen wrote: >> External Email - Use Caution >> >> Dear Freesurfers, >> I am running resting state analysis. I have TR 2.3, and 209 time points/frames, total length of the scan 483 seconds. I don?t drop any frames from the beginning ( nskip = 0 ). >> >> For one subject, the last two time points are motion outliers. So my tpef file includes numbers 478.4 and 480.7. When I run selxavg3-sess, I get the error time point exlusion file exceed nframes. >> >> I can?t figure out where the bug might be. So once again I would really appreciate your help! >> Thanks >> Lauri Tuominen >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ------------------------------ > > Message: 3 > Date: Thu, 24 Oct 2019 03:29:14 +0000 > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Learning fsfast tutorial > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <a582080c-85f2-9a05-6dad-d4cfba600faf(a)mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > look in sess01/bold, you should see 001 and 002. Do you? > > On 10/22/2019 9:40 AM, Renew Andrade wrote: > > External Email - Use Caution > > Dear experts: > I am trying to run preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run > But the outcome is ERROR: no run directories found. > > What could be wrong? > If you need more information let me know! > > Sincerely, > Andrade. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Question re: Longitudinal processing stream transforms.
by Jamie Hanson 05 Nov '19

05 Nov '19

External Email - Use Caution Dear FS List, My group was trying to look at the overlap between cortical labels in the longitudinal processing stream and I had a question re: use of transform files. In brief, we followed the commands for the longitudinal processing stream, creating a "subject-specific" template for each participant ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing#WorkflowSu…, using FS v.6.0). We processed T1w images multiple times and now, we wanted to transform the time 1 and time 2 (native space) scans to their subject-specific template. We used the following commands-- mri_vol2vol --mov $INDIVIDUAL_SCAN_TIME1_DIR/sub-BNU_25864_001.long.sub-BNU_25864_template/mri/brain.mgz --o $INDIVIDUAL_SCAN_TIME1/brain_001_to_temp.mgz --lta $SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/transforms/sub-BNU_25864_001_to_sub-BNU_25864_template.lta --targ $SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/brain.mgz But when we did this for time 1 and time 2 scans, they were poorly aligned. I also used the lta file for template to 001, but again things were poorly aligned. Should we be using m3z files? Or combining different transforms? Any guidance or suggestions are deeply appreciated. Thanks much, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org

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Using individual FreeSurfer utilities without the whole package
by Mike Schmidt 04 Nov '19

04 Nov '19

External Email - Use Caution Cursory googling has not turned up a solution to this, but I expect it may have been asked before. I would like to use several FreeSurfer utilities (mri_convert, mri_binarize, mri_pretess, mri_tesselate, mris_convert) in a docker container to post-process existing FreeSurfer output files. Creating a full FreeSurfer docker container is easily done. But ideally, I'd like to keep the container as small as possible so I would like to avoid using the whole 6GB package. While the license seems to legally allow derivative works like this, I'm not sure how the individual executables check for the license file, what the dependencies are, how tangled the web of dependencies may be, etc. 1. Is this a supported use and/or solved problem that I just haven't found in my searching? 2. If not, does anyone have a reason to warn me away from wasting time going down this road? Thanks for the benefit of others' experience, Mike Schmidt

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Subtraction of Stroke Volumes
by Rellick, Stephanie 04 Nov '19

04 Nov '19

External Email - Use Caution Hi All, I am looking for some help. I am working with stroke subject MRIs. For initial processing, I have "healed" the brains by applying the mirror image of the unaffected side. Now what I want to do is to subtract out only the area in which my lesion overlaps with BA4 (anterior and posterior), and get the statistics for that area only. I have made all the surface labels, turned the lesion into a label, and even created the actual intersect label, but what I really need to do is take BA4, subtract out any overlap with my lesion label, create a new label with this overlap, and then use the mris_anatomical_stats command line to get the statistics for this area to check the change over time. I know there has to be a way to do this but I cannot seem to figure it out!! Thanks, Stephanie

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nuisance factors
by Georgina Angelopoulou 04 Nov '19

04 Nov '19

External Email - Use Caution Thank you very much Douglas, It worked! I have one last question: in case of Volume, age slope is not significant, yet eTIV slope appears significant. Is it possible to include both age and eTIV as nuisance variables, in order to control my analysis for age and eTIV? What would be the contrast in that case? Thanks once again, Georgina

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Fwd: Fw: glm error
by Amrita Bedi 01 Nov '19

01 Nov '19

External Email - Use Caution ---------- Forwarded message ---------- From: *abedi000(a)citymail.cuny.edu <abedi000(a)citymail.cuny.edu>* < abedi000(a)citymail.cuny.edu> Date: Thursday, October 31, 2019 Subject: Fw: glm error To: Amrita Bedi <amibedi273(a)gmail.com> Amrita Bedi *Biomedical Engineering - Class of 2018* *The City College of New York - CUNY* ------------------------------ *From:* abedi000(a)citymail.cuny.edu *Sent:* Thursday, October 31, 2019 12:02 PM *To:* Freesurfer(a)nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> *Subject:* glm error Hello Freesurfer developers, I ran a seed based resting stage functional analysis for 287 subjects using the isthmus of the cingulate as a seed and now have pcc.nii.gz files in each individual subject folder. I concatenated these pcc files and am trying to run an osgm but get the following error: ERROR: DOF = 0 The commands i ran for concatenating and glm are: for l in `cat sessidBOLD2`; do mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i $l/Bold/PCC_Bold1_L/bilat*/pcc.nii.gz; done mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/DATA/Amrita/2389/abedi /FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir The mriglmfit.log gave me the following: $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_ 1to547_TR3/FSFAST cmdline mri_glmfit --y 4D_VOLUME_OUTPUT.lh.nii.gz --osgm --surf fsaverage lh --cortex --label /run/media/amritabedilocal/ DATA/Amrita/2389/abedi/FSFAST_1to547_TR3/fsaverage/label/lh.cortex.label --glmdir all_subjects_lh_ic_pcc.TR3.glmdir sysname Linux hostname imaging5.vaboston.lan machine x86_64 user root FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_ 1to547_TR3/FSFAST/4D_VOLUME_OUTPUT.lh.nii.gz logyflag 0 usedti 0 labelmask /run/media/amritabedilocal/DATA/Amrita/2389/abedi/FSFAST_ 1to547_TR3/fsaverage/label/lh.cortex.label maskinv 0 glmdir all_subjects_lh_ic_pcc.TR3.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Thank you for your help.

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make_average_subject error
by Maxime Perron 31 Oct '19

31 Oct '19

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Discrepancy between thresholded surface and cluster labels
by Bronwyn Overs 31 Oct '19

31 Oct '19

External Email - Use Caution Dear Freesurfer mailing list, I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for the same fixed effect (saved from the LME), and thresholding at the FDR corrected p -value. The question I have is why are there such large swatches of the cortical surface in the row 2 images that are labelled as log10 p = 5, when they are not included in the most significant and largest clusters that were found in the cluster summary file? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ]

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Re: [Freesurfer] nuisance factors
by Georgina Angelopoulou 31 Oct '19

31 Oct '19

External Email - Use Caution Dear Douglas, Thank you once again for your reply and your help. Attached please find the fsgd file (CMTX_b.fsgd) including age row scores and the contrast file. The command line I used is the following: - mri_glmfit --y lh.CMTX_b.thickness.10.mgh --fsgd CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh --cortex --glmdir lh.CMTX_b_thickness.glmdir The output is the following: georgias-mbp:CMTX georgina$ mri_glmfit --y lh.CMTX_b.thickness.10.mgh --fsgd CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh --cortex --glmdir lh.CMTX_b_thickness.glmdir gdfRead(): reading CMTX_b.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 45.2083 12.1603 Class Means of each Continuous Variable 1 patientmale 38.7778 2 patientfemale 53.0000 3 controlmale 40.1667 4 controlfemale 51.8462 INFO: gd2mtx_method is dods Reading source surface /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX cmdline mri_glmfit.bin --y lh.CMTX_b.thickness.10.mgh --fsgd CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh --cortex --glmdir lh.CMTX_b_thickness.glmdir sysname Darwin hostname 192.168.1.32 machine x86_64 user georgina FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/lh.CMTX_b.thickness.10.mgh logyflag 0 usedti 0 FSGD CMTX_b.fsgd labelmask /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.CMTX_b_thickness.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.CMTX_b_thickness.glmdir Loading y from /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/lh.CMTX_b.thickness.10.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to lh.CMTX_b_thickness.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 160.248 Matrix condition is 182721 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 148239 voxels in mask Saving mask to lh.CMTX_b_thickness.glmdir/mask.mgh Reshaping mriglm->mask... search space = 73702.448371 ERROR: dimension mismatch between X and contrast Contrasts/age_sim.mtx X has 8 cols, C has 5 cols Please note that an equivalent error appears with grey matter volume and surface area. Thank you once again, Best, Georgina

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