Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

External Email - Use Caution Hi Andrei, I was referring to .bashrc file located in these directories: /root/.bashrc /home/'your_user'/.bashrc ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mai

Re: [Freesurfer] Freeview misaligned surfaces "warning matrixinverse failed"

External Email - Use Caution Hi Andrei and Freesurfer experts, We had the same problem in the past and we noticed there was an extra line in the .bashrc file of Ubuntu: export FS_DISABLE_LANG="true" Deleting this line solves the problem. The .bashrc file should contain only the f

[Freesurfer] Remove border vertices

External Email - Use Caution Dear experts, I would like to project a parcellation (annot file) onto the cortical surface removing or hiding the border vertices of the different labels of the parcellation. I thought that I can do that scripting but first I would need to know which

Re: [Freesurfer] PetSurfer - MG coregister

External Email - Use Caution Dear Rahul, I just used the wiki of the Freesurfer functions, the information is very complete. If you want to use Freesurfer, you can start by doing the cortical reconstruction process for each subject ( https://secure-web.cisco.com/1Lj_XzmtE_iAYreTtm

[Freesurfer] PetSurfer - MG coregister

External Email - Use Caution Dear experts, I am trying to do PVC on FBB-PET images using the following commands: " mri_coreg --s s_001 --mov s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta mri_gtmpvc --i s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta --psf 6 --seg gtmseg.mgz

[Freesurfer] NoPVC PET

External Email - Use Caution Dear experts, I would like to get a noPVC PET volume scaled by the intensity of the pons, then project it and apply standard surface-based analysis. On the PetSurfer website it says: ** If you do not want to perform PVC, you can just run mri_gtmpvc

[Freesurfer] resample anatomical mask

External Email - Use Caution Dear experts, I would like to downsample the GM mask, which is at 1mm isotropic voxel size (freesurfer subject space), at 3mm isotropic. What is the most efficient way to do it with freesurfer? Thank you in advance. Marina

[Freesurfer] SNR

External Email - Use Caution Dear experts, I would like to calculate the SNR by dividing the mean intensity of the signal of interest by the SD of the noise. To do this, I would like to create a small circular ROI and place it within the region of interest and a larger circular RO

[Freesurfer] vertex ID in the contralateral hemisphere

External Email - Use Caution Dear experts, I would like to know the corresponding vertex in the contralateral hemisphere of a given vertex. Do you have a function that allows me to know it? Thank you very much in advance. Best regards, Marina

[Freesurfer] Tissue fraction effects correction

External Email - Use Caution Dear FS experts, We are planning to correct for tissue fraction effects on T1w/T2w ratio images using PETsurfer, setting the point spread function estimate to zero. My questions are: 1. Does it make sense to correct for tissue fraction effects on T1w/

[Freesurfer] parallel make_average_subject

External Email - Use Caution Dear experts, I would like to create an average subject from a very large population. I am going to compute it on a computer with a lot of threads and I would like to know if it is possible to parallelize the make_average_subject function to try to sho

[Freesurfer] Building a model

External Email - Use Caution Dear experts, We run the following analysis in Freesurfer: *Group* (2 levels) x *X1* (continuous IV) x *X2 *(continuous IV) + *Sex *(categorical covariate) + *Age* (continuous covariate) We exported the vertex with the maximum statistic after applyin

[Freesurfer] results visualization

External Email - Use Caution Dear experts, Do you know what are the steps to follow to visualize a surface-map of freesurfer results in Caret? Thank you very much in advance. Best regards, Marina ___ Freesurfer mailing list Freesurfer@n

Re: [Freesurfer] bias field correction and intensity normalization

External Email - Use Caution Hi Matt, We always really appreciate your help and advice. Thank you very much for your answer, now we understand much better why it is correct not to apply this correction. Best, Marina ___ Freesurfer mai

[Freesurfer] bias field correction and intensity normalization

External Email - Use Caution Dear experts, I would like to create myelin maps calculating the T1w/T2w ratio. Should I apply bias field correction and intensity normalization (i.e., "nu correction" in the Freesurfer pipeline) to T1w and T2w images separately before calculating the

[Freesurfer] T2 T1 registration with mri_robust_register

External Email - Use Caution Dear experts, I would like to co-register T2 to T1 robustly, both images have a resolution of 0.65mm3. Firstly, I tried bbregister with the '--init-rr' flag, but this function doesn't allow to keep the native voxel resolution (i.e., 0.65mm3), changing

[Freesurfer] nu correction

External Email - Use Caution Dear experts, I would like to create myelin maps calculating the T1w/T2w ratio. Should I apply bias field correction and intensity normalization (i.e., "nu correction" in the Freesurfer pipeline) to T1w and T2w images separately before calculating the

Re: [Freesurfer] PVC to calculate myelin maps

ajspNVvXE-3tAtnO87o54yNOHGv77Cv41TBCisFGTpIttO8yQHYH98UwscMRW5WzKsD425FeG8aoL0xD4o_zi2edkEoIY2y1H6L1aggLPectASboZKHVwgZYfe_8dGfBTUAuA/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20210531> Yes, you can use PETsurfer. I would apply it to the ratio On 5/28/2021 10:25 AM, Marina Fernández wrote: External Email - Use Caution Dear experts,

[Freesurfer] myelin maps

External Email - Use Caution Dear experts, I want to calculate myelin maps using the ratio of T1w and T2w MRI images. I would like to perform a correction of partial volume effects to create the maps (Shafee, Buckner & Fischl, 2015)*, instead of creating the maps using HCP Pipel

[Freesurfer] PVC to calculate myelin maps

this. Matt. %%%%%%% Marina Fernández <https://secure-web.cisco.com/1jnEmX8pyslFDNAKq1ESVKhaVYgavR5DWrZDCQVw6EIjIeRPu8VsMW2BmjjGD5q-TEhUnOvxdrLSTT5-Y6k0YXgDL7svI9z3nYXjvFbLZ7RTupBSGPm81_9ITZGgKJJOgPJdln72nUn8_i_M0BwX5vAQJhvU59P4tJ425dDyWnDL

[Freesurfer] PVC to calculate myelin maps

External Email - Use Caution Dear experts, I want to calculate myelin maps using the ratio of T1w and T2w MRI images. I saw that the correction of partial volume effects can be used to create the maps (Shafee, Buckner & Fischl, 2015)*. Can I use the PVC functions of PetSurfer for

[Freesurfer] fspalm output

External Email - Use Caution Dear experts, I used the function fspalm to run permutations with the following options: fspalm --glmdir /my_glmdir/ --cft 1.3 --name palm --iters 1 --cwp .05 --onetail Checking the palmcofig.txt file that is generated as output, I realized that e

[Freesurfer] beta coefficients

External Email - Use Caution Dear experts, In addition to t and p-value, I would like to report the beta coefficient of the fixed effects in the following regression equation for the vertex showing the max statistic within the cluster that survived multiple comparison correction

[Freesurfer] report results

External Email - Use Caution Dear experts, In addition to t and p-value, I would like to report the beta coefficient of the fixed effects in the following regression equation for the vertex showing the max statistic within the cluster that survived multiple comparison correction:

[Freesurfer] beta coefficient of the fixed effects

External Email - Use Caution Dear Doug, In addition to t and p-value, I would like to report the beta coefficient of the fixed effects in the following regression equation for the vertex showing the max statistic within the cluster that survived multiple comparison correction:

[Freesurfer] fspalm contrasts {Disarmed}

External Email - Use Caution Dear experts, To correct multiple comparisons on the surface I'm using fspalm. I know that this command internally transforms the design contrast and desing matrix from the Freesurfer format to the fsl format so that FSL-PALM understands the input.

[Freesurfer] fspalm error : --sig2p-max unknown

External Email - Use Caution Dear experts, When I was running permutations with fspalm an error appeared because it couldn't find the --sig2p-max option when using mri_surfcluster internally. You can find below the terminal output. How can I fix this error? Thank you in advance

[Freesurfer] Multiple regression analysis

External Email - Use Caution Dear all, I am doing a multiple regression analysis with 3 covariates of interest. I know that for testing two-way and three-way interactions I must create new variables by multiplying the covariates of interest. As Freesurfer transforms continuous var

[Freesurfer] PET image format

External Email - Use Caution Dear experts! I am using PetSurfer and I have a PET dataset that is in ecat format (.v). I would like to convert the images to nifti format to start processing the data. What function can I use to convert the images? How can I check that the left-right

[Freesurfer] Display results with tksurfer

?l=freesurfer@nmr.mgh.harvard.edu&q=date:20201019> Not sure, we don't use tksurfer that much anymore. Have you tried freeview? You can run freeview with tksurferfv and the same tksurfer arguments (makes it easier) On 10/13/2020 5:03 AM, Marina Fernández wrote: External Email - Use Caution Dea

[Freesurfer] display results with tksurfer

External Email - Use Caution Dear Freesurfer experts, I would like to modify the values of the colorbar scale to display results in the inflated surface with tksurfer, in such a way that displayed values in the colorbar range from the minimum t- value detected to the maximum t val

Re: [Freesurfer] lobe annotation and stats file

ts -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.lobe.stats -b -a ../label/lh.lobe.annot fsm010 lh white On 9/8/2020 7:58 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I would like to get a .stats file this the volume and thickness of lobe annotation, s

[Freesurfer] lobe annotation and stats file

External Email - Use Caution Dear experts, I would like to get a .stats file this the volume and thickness of lobe annotation, so I am following the steps indicated in this link https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation. Specifically, I used these commands: m

Re: [Freesurfer] G_subcallosal region is missing

anding what is happening. Can you send three pics of > the inflated surface of same location, one with cortex.label, one with > aparc.annot, and one with aparc.a2009s.annot? Also, please remember to > include previous emails so that I have context, thanks > > On 9/3/2020 9:

Re: [Freesurfer] G_subcallosal region is missing

External Email - Use Caution Sorry for the misunderstanding Doug . I have checked the lh.aparc.annot on the surface and there is no G_subcallosal label in these subjects. In that region are the G_and_S_cingul-Ant label / S_pericallosal labels. On the other hand, the surface appear

Re: [Freesurfer] G_subcallosal region is missing

area? On 9/2/2020 6:09 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I have noticed that some subjects don't show the G_subcallosal region in the *h.aparc.a2009s.stats file. Do you know why is this happening? Is there a way to fix it? Thank you in

[Freesurfer] G_subcallosal region is missing

External Email - Use Caution Dear experts, I have noticed that some subjects don't show the G_subcallosal region in the *h.aparc.a2009s.stats file. Do you know why is this happening? Is there a way to fix it? Thank you in advance. Best regards, Marina

[Freesurfer] total vertices does not match between results and labels

External Email - Use Caution Dear experts, I am using the mri_surfcluster function to cluster the surface results: mri_surfcluster --subject fbb_average --mask mask.mgh --hemi lh --olab label --in sig_results_tvalues.mgh --thmin 0.001 When I count vertices different

Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

External Email - Use Caution Hi Bruce, The talairach transform is reasonable and the aseg segment the cc correctly. I run with freesurfer dev version the same command (recon all -autorecon-2wm -subjid post_006) and now I have more information about what could be the problem. The

Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

-- > Hi Marina > have you looked at the inputs to mri_fill? Does the aseg.auto_noCCseg.mgz and > the wm.mgz look ok? > Bruce > > On Wed, 27 May 2020, Marina Fernández wrote: > External Email - Use Caution De

[Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

External Email - Use Caution Dear Freesurfer experts, When I run "recon-all -autorecon2-wm -subjid post_006" I get the following error: ... # #@# Fill Tue May 26 16:13:33 CEST 2020 /usr/local/freesurfer/subjects/post_006/mri mri_fill

Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

External Email - Use Caution Thank you, Doug. That makes sense. Do you think in this case it is a good option to add the flag --illcond to run this analysis without getting an error? or is it better not to use the variable apoe in these statistical analyzes? What do you recommend

Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

External Email - Use Caution Hi Douglas, I email you the fsgd file and I have also sent it through FTP. Thank you for your attention. Best regards, Marina. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh

[Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

External Email - Use Caution Dear Freesurfer experts, I get the error that you can find at the end of this message when I am running mri_glmfit. Whenever I run an analysis in which the experimental design has more than 12 columns, I get the same error, whereas if the experimental

[Freesurfer] mri_glmfit error

External Email - Use Caution Dear Freesurfer experts, I get the error that you can find at the end of this message when I am running mri_glmfit. Whenever I run an analysis in which the experimental design has more than 12 columns, I get the same error, whereas if the experimenta

Re: [Freesurfer] convert MNI152 coordinates into vertex index

External Email - Use Caution Thank you for the information, Bruce and Thomas! Thomas, I think this utility is perfect! I tried it with fsaverage subject without problems. Do you think I can use this function to calculate the vertex of the fsaverage5 (instead of the fsaverage)? R

Re: [Freesurfer] convert MNI152 coordinates into vertex index

External Email - Use Caution Hi Bruce, Thank you very much for the information. It is very useful. I'm taking a look at both possibilities. Regarding the second option you gave me: you can just run through the list of vertices and find the one that is > closest to your MNI coord

[Freesurfer] convert MNI152 coordinates into vertex index

External Email - Use Caution Dear Freesurfer experts, I would like to convert the x, y, z MNI152 coordinates into the vertex index of the fsaverage5. I would like to do it with a function that can give me the vertex index as output, because I would like to use this information in

[Freesurfer] convert gii to mgh/nii.gz (freesurfer surface)

External Email - Use Caution Hi experts, How can I convert a surface in .gii format to a surface in .mgh or nii.gz format? I tried with mris_convert but it doesn't work. Best regards, Marina ___ Freesurfer mailing list Freesurfer@nmr.

[Freesurfer] vertex number to MNI coordinates

External Email - Use Caution Dear Freesurfer experts, I hope you can help me with the following questions: 1. What is the best way to know the MNI coordinates to which a vertex of a surface corresponds? 2. I have projected the surfaces of the subjects onto the average subject fr

Re: [Freesurfer] sphere.reg file

External Email - Use Caution These are the previous emails: 1 » » » » » » » » » » » » Dear freesurfer experts, I run the following commands to perform analysis with projected surfaces on my average subject: make_average_subject --out my_avg_subject --fsgd fsgd.txt surf

Re: [Freesurfer] sphere.reg file

External Email - Use Caution We are using Freesurfer v6.0 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] sphere.reg file

External Email - Use Caution Dear freesurfer experts, I run the following commands to perform analysis with projected surfaces on my average subject: make_average_subject --out my_avg_subject --fsgd fsgd.txt surfreg --s s_001 --t my_avg_subject --o my_avg_subject.sphere.reg

[Freesurfer] Segmentation problem

External Email - Use Caution Dear Freesurfeer experts, After running the recon-all, a part of the temporal lobe of one subject was removed. I used the watershed algorithm to be less agressive in the skull stripping step: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatl

[Freesurfer] skull stripping problem

External Email - Use Caution Dear Freesurfeer experts, After running the recon-all, a part of the temporal lobe of one subject was removed. I used the watershed algorithm to be less agressive in the skull stripping step: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatla

Re: [Freesurfer] surfreg function

External Email - Use Caution Hi Doug, Thank you for your replay. I understood that if I did not specify "--surfreg my_avg_subject.sphere.reg" mri_preproc was going to use the original file ( sphere.reg), because in the help of mri_preproc it mentions this: --surfreg SurfReg : d

[Freesurfer] nopvc.nii.gz

External Email - Use Caution Dear Freesurfer experts, I have compared the PVC uptake values of gtm.stats with the values of gtm.nii.gz (that I loaded with the function load_nii in matlab). I realized that the values in matlab are transposed, i. e., the first value in gtm.stats is

[Freesurfer] surfreg function

External Email - Use Caution Hi experts, I am running the following command to create de average subjecto with Freesurfer v6.0: make_average_subject --out my_avg_subject --fsgd fsgd.txt Then, I want to do surface analysis with the thickness of each subject projected o

Re: [Freesurfer] Volume to 5th order icosahedron tesselation Surface (with PET images)

External Email - Use Caution Hi Doug, We thought it would be better to use 5th order icosahedron tesselation for PET because the resolution of the volume is lower: If, for thickness analysis, we carry the structural volumes with a resolution of 1x1x1 to ico7 on the surface, with P

[Freesurfer] Volume to 5th order icosahedron tesselation Surface (with PET images)

External Email - Use Caution Hi experts, This is a question related to PetSurfer steps. I would like to know if it is correct to sample the mgx volume onto the surface of the average subject of my dataset (created with 5th order icosahedron tesselation) instead of the fsaverage (

Re: [Freesurfer] Problem with registration (PetSurfer)

External Email - Use Caution Doug, the full terminal output from the terminal after running tkregisterfv was: freeview -transform-volume -viewport cor -v /usr/local/freesurfer/subjects/s_001/mri/orig.mgz:visible=0:name=orig.mgz(targ) /home/sleep2014/0_Analisis_Marina/PET/s_001_PE

Re: [Freesurfer] Problem with registration (PetSurfer)

External Email - Use Caution The error was shown after running tkregisterfv. Marina. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Problem with registration (PetSurfer)

External Email - Use Caution Dear experts, I am following PetSurfer steps (https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer). Something was wrong using mri_coreg function because when I checked the registration with tkregisterfv this error was shown in the terminal: *Warning

Re: [Freesurfer] Oval shape in average subject inflated

External Email - Use Caution It works! Thank you very much Bruce! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Oval shape in average subject inflated

External Email - Use Caution Is there something wrong? > Dear Freesurfer team, > > I created the FS average subject of the same dataset with 5th and 6th order icosahedron tesselation using the following commands: > make_average_subject --fsgd fsgd.txt --ico 5 --out avg_subject

Re: [Freesurfer] average subject with 5th order icosahedron tesselation

External Email - Use Caution That's it! Thank you Doug! Best wishes, Marina. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] average subject with 5th order icosahedron tesselation

External Email - Use Caution Dear Freesurfer experts, Now, I would like to downsample the average subject of a dataset (that is a 7th order icosahedron tesselation) to have surfaces with 10242 vertices (5th order icosahedron tesselation). How can I do that? Thank you in advance.

Re: [Freesurfer] Projection on fsaverage5

External Email - Use Caution Hi Doug, Thank you for your advice. I checked the results using ico 5 and fsaverage5 and it seems to have exactly the same values, but we are going to use --trgsubject fsaverage5, as you told me. On the other hand if we use EPI that it is coregiste

[Freesurfer] Projection on fsaverage5

External Email - Use Caution Hi Bruce, Thanks for the quick response. I found that the problem was the input. If I use the EPI that it is coregistered to the T1 of Freesurfer instead of the EPI that it is also normalized to the MNI space, it works and I can project the surface (t

[Freesurfer] Projection on fsaverage5

External Email - Use Caution Dear Freesurfer experts, I would like to convert the individual preprocessed EPI volume (that it is normalized to MNI152 space and without smoothing) to surface and project it on fsaverage5. I used the following command: mri_vol2surf --mov EPI.nii --r

[Freesurfer] Fill holes in BOLD surface

External Email - Use Caution Hi Freesurfer experts, I have projected 4D-preprocessed BOLD data to Freesurfer cortical surfaces. Resulting individual surfaces have many holes (see attached image) that I would like to fill with nearest neighbors values around each hole (avoiding the

Re: [Freesurfer] Conversion fMRI volumes to surface

External Email - Use Caution Thanks Doug. I created the surface with the command line that I sent you (mri_vol2surf ...) and then, I run that command that you sent me (tkregisterfv...) but I have the following error when freeview is trying to load the file: 'Failed to load MRI /

[Freesurfer] Transform LIA orientation to RAS

External Email - Use Caution Dear Freesurfer experts, How can I transform an EPI-surface with LIA orientation to RAS orientation? Thank you in advance. Best regards, Marina. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu ht

Re: [Freesurfer] Conversion fMRI volumes to surface

External Email - Use Caution Thank you Doug/Bruce. We would like to project our AFNI preprocessed EPI scans (T1-registration, motion correction, linear regression, but unsmoothed) to Freesurfer cortical surfaces in order to obtain one file containing 250 (number of dynamics) EPI-c

[Freesurfer] Conversion fMRI volumes to surface

External Email - Use Caution Dear experts, I’ve done the fMRI preprocessing and now I would like to convert each file (that contains 250 volumes) to surface. Is it correct to use the function mri_vol2surf? Should I use any specific flag because they are 4D files? What is the best

[Freesurfer] Problem with the segmentation of subregions

External Email - Use Caution Hi experts, We are doing the segmentation of the subfields of the hippocampal and amygdala subfields, brainstem subestructures and thalamic nuclei. When we used segmentHA_T1.sh and segmentThalamicNuclei.sh, 'Command not found' appears. On the other ha

[Freesurfer] (no subject)

External Email - Use Caution Hi experts, We are doing the segmentation of the subfields of the hippocampal and amygdala subfields, brainstem subestructures and thalamic nuclei. When we used segmentHA_T1.sh and segmentThalamicNuclei.sh, 'Command not found' appears. On the other ha

Re: [Freesurfer] ERROR gtmseg

External Email - Use Caution Dear Douglas, Did you get the subjects? I hope I loaded them correctly. Best regards, Marina. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

Re: [Freesurfer] ERROR gtmseg

External Email - Use Caution Dear Douglas, I put the subjects yesterday. They are: qsm_04_yr3 (it is the first subject with problems and we have another copy that is solved) and mci13_hsp (it is the new subject with problems). Thank you very much for your attention. Marina. _

Re: [Freesurfer] ERROR gtmseg

External Email - Use Caution Dear Douglas, Thank you very much for the help. We could solve the problem with that subject but now we have a similar problem with another subject. In the previous case, we have only one problematic voxel in the skull, but now the label 75 (it shoul

Re: [Freesurfer] ERROR gtmseg

External Email - Use Caution Dear Douglas, Thank you very much for the help. We could solve the problem with that subject but now we have a similar problem with another subject. In the previous case, we have only one problematic voxel in the skull, but now the label 75 (it shouldn

Re: [Freesurfer] ERROR gtmseg

nd the aseg.presurf.mgz and see > where they are. If there are not any, then do the same thing with > aparc+aseg.mgz > > On 10/7/2019 4:54 PM, Marina Fernández wrote: > > External Email - Use Caution > Dear Douglas, > > Sorry! This is the previous information: >

Re: [Freesurfer] ERROR gtmseg

External Email - Use Caution Dear Douglas, Sorry! This is the previous information: > Dear Douglas, > > Thank you for the replay. > > I think so, I can't find the code 229 in any subject. > > I can't see anything strange in the aparc+aseg.mgz. The cerebral voxels have the normal

Re: [Freesurfer] ERROR gtmseg

External Email - Use Caution Dear Douglas, Thank you for the replay. I think so, I can't find the code 229 in any subject. I can't see anything strange in the aparc+aseg.mgz. The cerebral voxels have the normal segmentation and labels. Could it be a problem with the extracerebra

[Freesurfer] ERROR gtmseg

External Email - Use Caution Dear experts, The following error occurs with one subject when I am running gtmseg command: *Computing colortable* *ERROR: cannot find match for subcortical segid 229* *ERROR: mri_gtmseg -s qsm_04_year3 --usf 2 --o gtmseg.mgz --apas apas+head.mgz --no

[Freesurfer] Create no-skull brain with gray matter mask

External Email - Use Caution Dear experts, I need to get a no-skull brain. The automated no-skull brain has many errors and I was thinking that I could create it taking into account the gray matter mask (we segment manually, so the mask is accurate) in such a way that everything o

[Freesurfer] CSF MASK

External Email - Use Caution Dear Freesurfer experts, Is there any way to obtain a CSF mask in Freesurfer similar to that obtained with the SPM segmentation (see attached)? Thank you in advance. Best regards, Marina. ___ Freesurfer mai

[Freesurfer] CSF MASK

External Email - Use Caution Dear Freesurfer experts, Is there any way to obtain a CSF mask in Freesurfer similar to that obtained with the SPM segmentation (see attached)? Thank you in advance. Best regards, Marina. ___ Freesurfer mai

[Freesurfer] CSF mask

External Email - Use Caution Dear Freesurfer experts, Is there any way to obtain a CSF mask in Freesurfer similar to that obtained with the SPM segmentation (see attached)? Thank you in advance. Best regards, Marina. ___ Freesurfer mai

[Freesurfer] Maximum vertex value

External Email - Use Caution Dear Freesurfer Team, How can I get the maximum vertex value for each subject in a particular cluster? Thank you very much. Marina. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm