Freesurfer July 2018

freesurfer@nmr.mgh.harvard.edu

112 participants
165 discussions

converting a mask made in MNI space to subject space
by Sims, Sara A 26 Jul '18

26 Jul '18

External Email - Use Caution Hello, I am trying to put a mask that I made on the MNI brain (that had been run through recon) into individual subject space. I have already created a registration matrix using the following command: mni152reg --s $patient --o $registration/$patient/registermni_$patient.dat --1 --save-vol Now I want to apply this matrix but from MNI -> subject. So I tried doing this: mri_vol2vol --targ $patient/mri/orig.nii --mov $mnimask/net4splitmask_bin.nii --reg $registration/$patient/registermni_$patient.dat --o $outp/$patient/net4splitmask_bin.nii --nearest --rot 180 0 0 But it just spits back out the MNI mask ($mnimask/net4splitmask_bin.nii) in MNI space. I tried using -inv but realized that was wrong because then it just gave me the subject’s orig. How can I get it to actually put the MNI-space mask onto the subject’s brain? Sara

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Re: [Freesurfer] fcseed-config
by shahin＠nmr.mgh.harvard.edu 26 Jul '18

26 Jul '18

You need to run fcseed-sess to generate that. > Hi all > > > I am running a seed to whole brain connectivity analysis. I am using the > labels that I have made from functional ROIs. > > When I run fcseed-config, It makes the configuration file but not the .dat > files. > > Here is my command: > > fcseed-config -segid 1 -seg $SUBJECTS_DIR/${subj}/mri/lh.DIPS_sup2018.mgz > -segid 1 -seg $SUBJECTS_DIR/${subj}/mri/lh.DIPS_inf2018.mgz -segid 1 -seg > $SUBJECTS_DIR/${subj}/mri/rh.DIPS.2018.mgz -fcname bilateral_DIPS.dat -fsd > rest -rlf restruns -mean -cfg > ../all_subjects/${subj}/bilateral_DIPS.config -overwrite > > I appreciate if someone tells me how to fix it. > > Thanks > Mona > > > > Zahra (Mona) Nasiriavanaki > > Postdoctoral Research Fellow > > Martinos Center for Biomedical Imaging > > Massachusetts General Hospital > > 149 13th Street, 149-2615 > > Charlestown, MA, USA, 02129 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _____________________________________ Shahin Nasr Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown, MA 02129

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fcseed-config
by Nasiriavanaki, Zahra 26 Jul '18

26 Jul '18

Hi all I am running a seed to whole brain connectivity analysis. I am using the labels that I have made from functional ROIs. When I run fcseed-config, It makes the configuration file but not the .dat files. Here is my command: fcseed-config -segid 1 -seg $SUBJECTS_DIR/${subj}/mri/lh.DIPS_sup2018.mgz -segid 1 -seg $SUBJECTS_DIR/${subj}/mri/lh.DIPS_inf2018.mgz -segid 1 -seg $SUBJECTS_DIR/${subj}/mri/rh.DIPS.2018.mgz -fcname bilateral_DIPS.dat -fsd rest -rlf restruns -mean -cfg ../all_subjects/${subj}/bilateral_DIPS.config -overwrite I appreciate if someone tells me how to fix it. Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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petsurfer
by John Anderson 25 Jul '18

25 Jul '18

External Email - Use Caution Dear Petsurfer experts, I used partsurfer in FS6 and had applied partial volume correction (PVC) on PET data. I followed the same steps as in wiki which was very well explained! Thank you!. The analyses went fine... I would like to inquire about some issues, and I highly appreciate any clarification: 1. The flag --psf in "mri_gtmpvc": Is the value of "psf" means the amount of smoothing (fwhm in mm) that will be applied on the corrected maps? If I give "psf" a value of "zero", does this means that the corrected maps are no longer going to be smoothed? The motivation of the question is that I would like to smooth the images at the end of the analysis, so I can apply the amount of smoothing on the PVC images vs analysis involve non-pvc images. 2. For some of my group analyses, I don't see any difference between the groups. When I apply PVC using "mri_gtmpvc", I see difference in pathologically relevant regions, and vice versa for some other analyses where I see difference between the groups without PVC then the difference disappear following PVC. I highly appreciate if you please clarify why PVC can find results or eliminate findings. What is the idea of partial volume effect PVE in this case? 3. Group analysis: following PVC, I used "mri_concat" to combine the images "?.mgx.gm.nii.gz", then I smoothed the final combined images using the flag "fwhm" in "mri_surf2surf". I used fwhm=3mm and then fwhm=6mm. For all analyses I can see clusters of difference between the groups at fwhm=3mm. For some analyses the difference disappears when I use fwhm=6mm . Is this till a partial volume effect even after applying pvc or this is relevant to an extra smoothing effect which obscure the PET signal? is there any recommended fwhm value for PET images? Thank you for your guidance, John

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Re: [Freesurfer] Matched analysis with 2 controls 1 case weighting
by Dowling, Kevin Francis 25 Jul '18

25 Jul '18

Hi Doug, Thank you very much for your reply and my apologies for this belated response. The two approaches you mentioned were the only ones we could think that might work for a DV like cortical thickness. That being said, we were originally thinking of a repeated measures anova. However, (and I may be mistaken here) I believe that such an approach would need to be implemented in the Freesurfer longitudinal stream. However, I recently saw a thread in the archives that suggested this approach is not recommended if the T1 images are from matched subjects (as opposed to multiple scans from the same subject over time). Is that correct? As an aside, as we're hoping to separately look at matched subjects in three groups a bit later using a 1:1:1 match. If we should avoid the longitudinal stream, is there any other way to implement an RM anova in Freesurfer? Otherwise, I think we're hoping to move forward by averaging the 2 controls together with make_average_subject and then implement a paired analysis -- which was probably the more sound choice to begin with. Thank you again! Kind regards, Kevin > Douglas N. Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Mon, 16 Jul 2018 10:49:28 -0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> > >There is nothing to plug and play. I'm not even sure about the theory, >but I'd guess you'd use something like a repeated measures anova or >simply average the two controls together and do a simple paired test. Do >you know what the theory would be behind your statitical test? >On 07/09/2018 01:27 PM, Dowling, Kevin Francis wrote: >> >> Hello Freesurfer Experts, >> >> >> I'm writing with a quick question about matched analysis. >> >> >> We have a cohort of MRI data collected such that there are two >> controls for each case, and these 2 controls are each matched to a >> specific case using a propensity score algorithm (~400 subjects >> total). For our analysis, we would like to try to implement a matched >> (or paired difference) analysis of cortical thickness (across the >> whole surface, not .aparcs) in Freesurfer. However, based all the >> documentation I have been able to find it seems that FS permits only >> paired difference analyses using matched pairs. Is this correct? Might >> there any way to implement such an analysis in Freesurfer using >> matched trios instead? >> >> >> We are open to using any Freesurfer version for this analysis, >> including dev, though the scans are currently reconned with FS 5.3. >> >> >> Thank you so much for your consideration! >> >> >> With kind regards, >> >> Kevin >> >> >> *Kevin F. Dowling * >> Clinical Research Coordinator >> Brain Genomics Laboratory >> Division of Psychiatric Neuroimaging >> Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> 149 13th Street >> Charlestown, MA, 02129 >> (p) 617.643.3215 >> Pronouns: He / Him / His >> >> >> _______________________________________________ >> 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 Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.3215 Pronouns: He / Him / His

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mris_ca_label seed
by Rosemary Nicholas 24 Jul '18

24 Jul '18

External Email - Use Caution Hello, I am running a dataset through version 6.0 of Freesurfer on Linux, extracting results for both the Desikan atlas and our own atlas. When extracting the stats for our atlas, the results were varying considerably (sometimes up to 10%) in test-retest runs. The release notes for 4.5 indicate that the default setting for mris_ca_label should use the same number as a seed, and therefore give the same results, but it doesn't. "The binaries in the recon-all stream which are subject to variability due to usage of a random number generator (mris_smooth, mris_sphere, mris_topology_fixer, mris_topo_fixer and mris_ca_label) are now seeded with the same number, with the result being that repeated runs of the recon-all stream on a subject on the same platform will always give identical results." The issue seems to be resolved by adding -seed 1234 as a flag to mris_ca_label. I would like to understand what this is actually doing though, before applying it to all my data. What is the random number generator used for? What does setting it to 1234 actually do? It isn't listed in the optional flagged arguments. Is it just deciding which vertex is labeled first? Here is how we are running it (in two independent scripts): FIRST: # autorecon1 including data conversion recon-all -i $mprage/001 -autorecon1 -subjid $s # autorecon2 with threshold adjustments recon-all -seg-wlo 60 -seg-ghi 70 -autorecon2 -subjid $s # autorecon3 recon-all -autorecon3 -subjid $s THEN: mris_ca_label $s $h sphere.reg /g5/dcn/freesurfer_testing/subjects/"$h".rantaFL.gcs rantaFL.annot modified to: mris_ca_label -seed 1234 $s $h sphere.reg /g5/dcn/freesurfer_testing/subjects/"$h".rantaFL.gcs rantaFL.annot Thank you, Rosemary Nicholas Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute

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Convert to .nii in the native space including all changes in the pial surfaces
by Sofia Rodriguez Penuela 24 Jul '18

24 Jul '18

External Email - Use Caution Hello team, We have first fixed non-cortex voxels in the pial surface using the brainmask.mgz volume, and we next corrected pial surfaces that mistakenly included cerebellum by creating a copy of 'brain.finalsurfs.mgz' named 'brain.finalsurfs.manedit.mgz' and erase problematic voxels in it . All these changes appeared correctly in brain.finalsurfs.mgz after running autorecon-pial in the two steps. How could I get a .nii file containing all these changes in the native space (0.65x0.65x0.65)? Thank you! -- Sofía Rodríguez Peñuela, Técnico de Laboratorio. Laboratorio de Neurociencia Funcional Departamento de Fisiología, Anatomía y Biología Celular. Universidad Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - España - Movil: 627273085 Email: srodpen(a)upo.es http://www.upo.es/neuroaging/es/

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Surfaces misaligned "Did not find any volume info. Warning: MatrixInverse failed".
by Sofia Rodriguez Penuela 24 Jul '18

24 Jul '18

External Email - Use Caution Dear Freesurfer team, After loading a volume in Freeview, we try to load surfaces, but surfaces are shown misaligned (see attached image) and the Command Console shows the following error: "Did not find any volume info. Warning: MatrixInverse failed". This happens with all subjects. If those subjects are open with tkmedit, the software does not show any error. Freesurfer v6.0 and Freeview are updated correctly. We use Ubuntu 16.04. Can you help us to solve this problem? Do you know the solution? Thank you -- Sofía Rodríguez Peñuela, Técnico de Laboratorio. Laboratorio de Neurociencia Funcional Departamento de Fisiología, Anatomía y Biología Celular. Universidad Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - España - Movil: 627273085 Email: srodpen(a)upo.es http://www.upo.es/neuroaging/es/

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tkregister2 scripting- help with saving reg.dat
by Yagmur Ozdemir 19 24 Jul '18

24 Jul '18

External Email - Use Caution Hello freesurfer experts, I am editing the registration matrix between two volumes (fsaverage's T1 to fit MNI152 from fsl) using tkregister2, and I cannot save the registration because I do not have permission to change the .dat file I originally opened with tkregister2. I cannot change the permissions. I do not want to lose all the editing I have done so far, so would really appreciate if someone could give me advice on how to save the registration as a seperate file either in GUI or from terminal. FYI, I know ideally I shouldn't need to edit the registration but for some reason I had weird flipping issues when using mri_vol2vol and mni152.register.dat with --inv option. Also the system for some reason does not recognize a binary volume with the --interp nearest option, so fills in the whole volume. I would appreciate any suggestions. Best Idil

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Aparc.stats based on fsaverage?
by Martin Steppan 24 Jul '18

24 Jul '18

External Email - Use Caution Dear Freesurfer/s, Sorry, it might be a stupid question, since I am a newbie in this field. Is the ?.aparc.stats file somehow based on transformation to fsaverage space? I am aware that this is the case for -qcache, but is this also true for the predefined ROI results? I am asking, because we also have juvenile brains, and transformation to the average adult brain could be a problem. Does anyone have useful information for me? Best wishes, Martin

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Freesurfer July 2018