Freesurfer November 2019

freesurfer@nmr.mgh.harvard.edu

87 participants
122 discussions

recon-all -s SOME_SUBJECT exited with ERRORS
by Emanuel Alvaredo 07 Nov '19

07 Nov '19

External Email - Use Caution Hello FreeSurfer Developers, I am running de following command /usr/local/freesurfer/subjects/SOME_SUBJECT /usr/local/freesurfer/bin/recon-all -s SOME_SUBJECT -i /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 - all -parallel I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. I have checked the log but I dont find de cause. 1) FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thanks in advance Emanuel

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Help with "orig.mgz"
by Fernando Castellano 07 Nov '19

07 Nov '19

External Email - Use Caution good afternoon, I am using freesurfer for my thesis in image technician. I would like to know specifically what the orig.mgz file is? I have read that it is step 1 of re-conall. But I don't fully understand thank you, best regards

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Re: [Freesurfer] LME model contrast matrix (Diers, Kersten /DZNE)
by Liu Guodong 07 Nov '19

07 Nov '19

External Email - Use Caution Hi Kersten, Thank you so much for the reply and that helps a lot. There are still some questions that I hope you can help me. 1.For the first model in you last email, you said 'To get the mean for group B, one would need to add the beta weights of the two regressors.’. I wonder if the beta weights should be 1 for regressors1 and 1 for regressor2, and the mean for group B is regressor2 plus regressor1 with the condition the value of group B is bigger than group A. 2.Is there any P-value for the lme_fit_FS function to present the quality of the fitting? 3.As you said before, if I have 3 group A,B,C for this model, and group A is reference group, the regressor1 is the mean of group A, and regressor2 and 3 reflect the difference between group A and B,C. But if I want to know the difference between B and C, what should I do. From the F-test, there only have a P-value to reflect how different between group B and C, I wonder can I compute a value the same as regressor 2 to reflect the difference? Thanks! Best regards, Guodong > > ------------------------------ > > Date: Tue, 5 Nov 2019 09:48:06 +0000 > From: "Diers, Kersten /DZNE" <Kersten.Diers(a)dzne.de> > Subject: Re: [Freesurfer] LME model contrast matrix (Diers, Kersten > /DZNE) > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <1572947286.4016.34.camel(a)dzne.de> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hello Guodong, > > consider as an analogy a two-sample t-test, where we simply compare two > groups A and B: > > If formulated as a regression problem, a commonly used model matrix for > this test (but others are possible, too) will consist of two columns, > one being all ones (the intercept), the other being zero for group A > and one for group B. > > The beta value for the first regressor should reflect the mean for > group A (which is chosen as the reference group), and the beta value > for the second regressor should reflect the difference between group A > and B, which is the primary interest for this comparison. To get the > mean for group B, one would need to add the beta weights of the two > regressors. > > The LME design matrices follow the same logic. > > Alternatively, as said before, other design matrices are possible. In > the above toy example, one could also use a matrix with two columns, > where column 1 is one for group A and zero for group B, and column 2 is > zero for group A and one for group B, thus omitting the overall > intercept. Then, the beta weights would directly reflect the means of A > and B. To get the difference between groups A and B, one would need to > subtract the beta weights. > > Mathematically, the two above models are equivalent. This also implies > that one should not specify a model where there is an intercept, a > regressor for group A, and a regressor for group B, because in this > case, the regressors would be linearly dependent. Since having an > overall intercept is advantageous (especially in more complex modelling > situations than this toy example), the first model is the preferred > one. > > Hope this helps, > > Kersten > > > On So, 2019-11-03 at 16:33 +0800, Liu Guodong wrote: >> ????????External Email - Use Caution???????? >> >> Dear Kersten:? >> The ?1 and ?2 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 >>> >>> Date: Thu, 24 Oct 2019 08:06:28 +0000 >>> From: "Diers, Kersten /DZNE" <Kersten.Diers(a)dzne.de> >>> Subject: Re: [Freesurfer] LME model contrast matrix >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.ed >>> u> >>> Message-ID: <1571904388.10840.18.camel(a)dzne.de> >>> Content-Type: text/plain; charset="utf-8" >>> >>> ???????External Email - Use Caution???????? >>> >>> Hi Guodong, >>> >>> On Di, 2019-10-22 at 16:05 +0800, Liu Guodong wrote: >>>> >>>> ????????External Email - Use Caution???????? >>>> >>>> Hello FreeSurfer Developers, >>>> >>>> I'm doing the LME tutorial, and I have some questions . >>>> >>>> 1. Why don?t we need to put the healthy controls in the designed >>>> matrix X? >>> Because that would be mathematically redundant, given the intercept >>> and >>> the other group regressors.? >>> >>> In general, one chooses a reference group (in this case, controls), >>> and >>> this group is implicitly modeled (by the intercept). The other >>> group >>> regressors will then model the difference between that particular >>> group >>> and the reference group. >>> >>>> >>>> 2. What?s the interpretation of the first row of the contrast >>>> matrix >>>> [1 0 0 0 0], does it mean first group minus healthy group? >>> I assume that we are talking about the first example, i.e. the >>> simple >>> univariate case (not mass-univariate). >>> >>> Just to be precise, the first row of the contrast matrix would be >>> [ 0 0 0 1 0 0 0 0 0 0 0 0 0 0], right? >>> >>> The fourth regressor (which this contrasts tests) is "colum 3 * >>> time", >>> i.e. the interaction between the first group and time. This would >>> indicate to which extent the slope across time in this group is >>> different from the slope of the reference group. >>> >>>> >>>> 3. There is a pvalue and a vector sgn from the result of F-test, >>>> I >>>> know the interpretation of the sgn, but I don?t know the >>>> hypothesis >>>> of the pvalue, could you please help me with that? >>> Strictly speaking, we test (and try to reject) the null hypothesis >>> that >>> the ?parameter estimate (or a linear combination of parameter >>> estimates) is zero. >>> >>> Best regards, >>> >>> Kersten >>> >>>> >>>> Thanks in advance! >>>> >>>> Best regards, >>>> Guodong >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> ------------------------------ >>> >> > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 189, Issue 5 > ******************************************

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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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Freesurfer November 2019