Re: [Freesurfer] mri_surf2surf --projfrac error: cannot spec both --sval-xyz and --sval

Dont use --trgicoorder. Also, smooth the input, not the output (ie, use --fwhm not --fwhm-trg). Don't use projfrac there (which will fix the --sval-xyz error). Your 2nd command looks the same as the first On 9/27/20 10:30 PM, 谢娆 wrote: External Email - Use Caution Hi, To begin with,

Re: [Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output

It's been a while since 5.3, but I vaguely remember something like this happening because there were one or two super bright voxels in the image. If this is the case, then you can find them and clip them. On 9/18/20 10:32 AM, Fischl, Bruce wrote: I don’t think adding 100 will work as once it

Re: [Freesurfer] Recon-all crooked volumes

I don't think there is anything wrong with it. The subject just has his/her head tilted a fair amount in the scanner. The final analysis looks ok from here On 9/17/20 1:14 PM, Hasimoglu, Yasemin wrote: Hello, I recently ran recon-all on a group of subjects with FreeSurfer 7.1.0, and for one

Re: [Freesurfer] Prescan normalize and freesurfer

#2 is the safest. I think #1 is probably ok, but you'll want to check that the 12% does not correlate with some factor of interest (eg, all 12% in the control group) On 9/17/20 8:12 AM, Mikolas, Pavol wrote: External Email - Use Caution Dear Freesurfer Developers, I am analyzing the

Re: [Freesurfer] peak MNI coordinates within a masked sig.mgh

If you know the vertex number, then you can get the RAS in "tkregister space", eg, in freeview (other ways too),  then use #2 on that page On 9/17/20 4:18 AM, Fred Sampedro wrote: External Email - Use Caution Thank you very much Prof Greve! I'm almost done! Now, using mri_volcluster

Re: [Freesurfer] Make BEM with corrected brainmask

Try mris_expand On 9/16/20 10:24 PM, Kadwani, Manorama wrote: Thank you, I got a brain surface using the mri_binarize function. Is there a function for expanding the surface radially by a few millimeters? I want to create the inner skull surface as an expansion of the brain surface. Thanks,

Re: [Freesurfer] Cohen's D calculation and interpretation

You have created a circularity that is classic in neuroimaging (see Vul's paper on "VooDoo Correlations"). By using only voxels inside a cluster, you have selected voxels that are sure to show hi D values On 9/16/20 7:48 PM, Alejandro Meruelo wrote: > External Email - Use Caution > > Hi

Re: [Freesurfer] Resting state fMRI preproc-sess registration error

Can you send the commands you used to check the registration ? On 9/16/20 2:24 PM, Wenzhen Zhao wrote: > External Email - Use Caution > > Dear freesurfer developers, > > I am working on preprocessing resting state fMRI and used the following > command. > > $ preproc-sess -s sess01 -fsd r

Re: [Freesurfer] left-right flip?

I'm sorry to hear it, but at least you figured it out. You're best option is just to convert directly from the dicoms if you have them using mri_convert, dcmunpack, or just passing a dicom file directly to recon-all as input. If you don't have access to the dicoms, you can run mri_convert input

Re: [Freesurfer] papers that have reported results using FS5.2

I can't remember what the issues where, but I don't think they were all that bad, something with surface placement. Bruce might remember better than me On 9/15/20 7:22 PM, Paul wrote: External Email - Use Caution Dear Freesurfer Developers, With Freesurfer 5.2 being listed as depreca

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

In both cases, the surfaces are placed on the high-resolution images. I'm not sure whether volume segmentation (ie, aseg) of highres images is better than at 1mm. On 9/9/20 10:30 AM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Falk and Doug, thx for clarifying.  Before

Re: [Freesurfer] midline to cut the brain stem into Left and Right

Not that I know of, sorry On 9/1/20 10:20 AM, 刘梦醒 wrote: External Email - Use Caution Hi Freesurfer group, For some reason, I have to use the left and right brain stem separately. I wonder if there is one way to have a midline, to cut the brain stem into Left and Right? Many thanks

Re: [Freesurfer] recon-all error

Try running it with --no-surfs On 8/29/20 12:34 PM, Jie Zhao wrote: External Email - Use Caution Hi, Douglas I first heared the tkregisterfv, tryed the tkregisterfv --fstal --s mprage the output error was this: ERROR: cannot find /usr/local/freesurfer/subjects/mprage/surf/lh.whi

Re: [Freesurfer] recon-all error (incorrect orientation)

You can use the Transform volume tool in FreeView, though it will be a pain if you have to do a bunch. Getting the original dicoms is a much better place to start. On 9/1/20 9:13 AM, Ellen Ji wrote: External Email - Use Caution Dear Bruce (and Jie), I believe I am encountering the same proble

Re: [Freesurfer] tkregister2 deprecated for FS7.1?

In 7.1.1, you can use tkregisterfv instead of tkregister2 (same command line otherwise).  If you don't want to download 7.1.1, you can get just tkregisterfv from https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv On 8/31/20 3:42 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote

Re: [Freesurfer] mri_preproc error with FS6.0

Why are you specifying the target as average instead of fsaverage? On 8/31/20 12:13 PM, chelseach...@yahoo.com wrote: External Email - Use Caution Hello, I am running into an error while running the LGI analyses using FreeSurfer 6.0 following Jove article recommendations ( https://ww

Re: [Freesurfer] mris_anatomical_stats

Yes, that is the effect of including the cortex.label On 8/31/20 8:28 AM, Palin, Tara wrote: External Email - Use Caution When using the following command line: mris_anatomical_stats -th3 -mgz- cortex ../label/?h.cortex.label -f ../stats/?h.aparc.pial.stats -b -a ../label/?h.aparc.a

Re: [Freesurfer] Schwartz atlas reference in recon-all 3T flag

No, not published. Probably won't be. It has a small effect on the output anyway On 8/31/20 1:47 AM, Hye Min Shin wrote: External Email - Use Caution Hello, I understand that from a previous FreeSurfer question the Schwartz atlas used in the 3T flag during recon-all is not published

Re: [Freesurfer] One hemisphere recon-all and aparc+aseg.mgz

There is a bug in recon-all when trying to only run with one hemi (actually there are several bugs). Currently, it is failing at mris_volmask, which needs to have --lh appended to the command line. You can do this with an expert options file. This is  simple text file that should have the conte

Re: [Freesurfer] recon-all exited with errors

Try looking at our wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview On 8/30/20 7:16 AM, Vinny K wrote: External Email - Use Caution Hi, I've tried to process a scan but it gets hung up on a particular large defect and then exits with error.  I've

Re: [Freesurfer] Petsurfer - negative values after RBV partial volume correction

Yes, this is not unusual. The GTM (which RBV is based on) is just a GLM where it uses a linear model to estimate the ROI intensities. There are no constraints on positivity. When the model is not exactly correct (which it never will be) it is possible to get negative values. Usually this only h

Re: [Freesurfer] Covariates vs sample size

Yes, you will have enough DOF if that is what you are asking On 8/28/20 4:31 AM, Sunil Khokhar wrote: External Email - Use Caution Dear Experts, With a sample size of 45, can I perform GLM analysis with one primary independent variable and 6 covariates? Dependent variable is cortica

Re: [Freesurfer] Global surface area and global thickness values {Disarmed} {Disarmed}

Yes! On 8/26/20 9:30 AM, Palin, Tara wrote: External Email - Use Caution Again, thank you for your explanation of how these variables are calculated. However, the the main question still left is, are these values the most representative of the whole cerebral surface area and the who

Re: [Freesurfer] Questions about speed up the longitudinal processing

Rather than -parrallel, use -threads to indicate the number of processors to use On 8/5/20 10:47 AM, Yang Molly wrote: External Email - Use Caution Hi list, I tried to run some longitudinal data with two time points with the latest version Freesurfer (7.1.0) on the Ubantu 16 system.

Re: [Freesurfer] PetSurfer Crashing

Did you really mean to pass subject/mri/gtmseg.lta ? The registration is supposed to be the registration of the input (PET.template.nii.gz) to the anatomical. subject/mri/gtmseg.lta is the registration of gtmseg.mgz to the anatomical. On 7/20/20 11:21 AM, Crawford, Anna wrote: Extern

Re: [Freesurfer] Fwd: One hemisphere recon-all ERROR

sorry, I thought I answered this a while back. Try using -hemi lh instead of -lh On 7/18/20 1:22 PM, Alina Rojas wrote: External Email - Use Caution Hello Freesurfer community, I was wondering if you could look at the e-mail below. Thank you! Alina Anfang der weitergeleiteten Nach

Re: [Freesurfer] Right and left on MRI scan and on images

This information is extracted out of the dicom header, so as long as you are converting directly from dicom, the information will be correct. You can run mri_info orig.mgz and it will print out a lot of information, including the orientation string. Eg, RAS means that the fastest (column) dimen

Re: [Freesurfer] mris_convert error

Do you mean that the inflated is not somehow in line with the pial? They are not supposed to be (and it is not clear what that would mean). The white and pial look aligned On 7/6/20 7:16 AM, Mason Wells wrote: External Email - Use Caution Hi Experts, I am using mris_convert to conve

Re: [Freesurfer] Destrieux atlas volume based in matlab

you can run recon-all on the MNI152 itself, though it will not reflect the average of the subjects that went into it On 7/3/20 4:42 AM, Gian Marco Duma wrote: External Email - Use Caution Dear Freesurfers experts, I need to obtain in the volume and not in the surface, in MNI space wi

Re: [Freesurfer] Recon-all 5.3.0 failing and I can't see the error message

Do all subjects have this problem or just this one? Have you looked at orig.mgz to rule out any major problems? On 6/30/20 8:13 AM, Ian wrote: External Email - Use Caution Here you go Doug, thanks. docker@7d97b79d7546:/execute/freesurfer2016/mri$ mri_nu_correct.mni --n 1 --proto-ite

Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}

If you want to save it on label format, then mri_cor2label is the right way to go. Make sure to use the --surf option. If you want them in separate mgz files, then use mri_binarize with --match On 6/12/20 7:35 PM, Mason Wells wrote: External Email - Use Caution Hi Doug, Yes, I mean

Re: [Freesurfer] Longitudinal edits on norm.mgz instead of brainmask

Which edits did you make? Control points are not linked to a volume and will be applied appropriately. Or did you make edits meant to fix the mask? On 5/17/20 4:29 AM, Elena Pozzi wrote: > External Email - Use Caution > > Dear experts, > > I have a longitudinal study with 2 time points a

Re: [Freesurfer] Group Analysis Covariates

And what is your new question? On 5/17/20 12:10 PM, Hua, Jessica wrote: External Email - Use Caution Sure, attached are the files again and here is our previous correspondence: Original question: After running the permutation and finding significant clusters, I am trying to calcul

Re: [Freesurfer] Apply transformation

Yes, mri_vol2vol On 2/15/20 11:07 AM, Adam Rytina wrote: External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV

Re: [Freesurfer] About statistical analysis of volumetric results

It is valid to compare just the absolute volumes, but it might improve the results to divide by the ETIV. I would compute the average ETIV and divide by that. Alternatively, you can compute a relative change (vol2-vol1)/((vol1+vol2)/2) On 2/15/20 10:23 AM, Halil Aziz VELİOĞLU wrote:    

Re: [Freesurfer] Overlay electric field distribution on pial surface

Did you look at the results of the registration to make sure that they are ok? But you probably don't need to run the registration anyway since the surfaces are in the T1.mgz space anyway. How are you verifying that the efield is properly aligned to the T1.mgz? Is it also 1mm^3 and 256^3? Doe

Re: [Freesurfer] Seeing the Results in the Original Space

check out this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 9/9/18 11:18 AM, Maedeh Khalilian wrote: External Email - Use Caution Dear FreeSurfer Experts, How can i have the results of FreeSurfer in its original space? The results have rotation and also the a

Re: [Freesurfer] recon-all error

on this email. I’m not so sure what you mean by the terminal output file? Thanks, Da-Yea *From:*freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* Friday, September 07, 2018 11:36 AM *To:* freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] FsPalm patch

Actually, I figured it out. Everything is there now, just follow the instructions in the README. On 9/7/18 11:48 AM, Douglas Greve wrote: > I have recreated the patch. The only problem is that I don't quite > remember what should be in it. The wiki says that there are 3 files to >

Re: [Freesurfer] FsPalm patch

I have recreated the patch. The only problem is that I don't quite remember what should be in it. The wiki says that there are 3 files to install, but I can only remember two. Tom, can you install those two files and run it and see what fails? That will tell me what the 3rd file is. thanks doug

Re: [Freesurfer] recon-all error

can you send the terminal output and recon-all.log? thanks On 9/7/18 9:58 AM, Song, Da-Yea wrote: External Email - Use Caution Hello, I’m running some subjects through recon-all but have noticed that some error out (terminate the job) within seconds of starting. Any suggestions woul

Re: [Freesurfer] fsaverage for a Left vs Right hemisphere Longitudinal

I'm not sure what this is referring to, but you should be very careful flipping images. If you want to compare left and right, then use the xhemi tool https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi On 9/4/18 10:41 AM, Martin Reuter wrote: Hi Xiaoyu, please keep the previous conversation as i

Re: [Freesurfer] NIFTI to pial.vtk space

what is your mris_convert command line? On 9/3/18 4:10 PM, M. Jordan wrote: External Email - Use Caution Hello, I have a CT NIFTI coregistered to the MRI NIFTI used for reconAll. When I export the .pial files to .vtk using mris_convert, they are shifted with respect to the MRI. Is t

Re: [Freesurfer] error using -taskreg

are you using matlab or octave? If matlab, which version? The problem appears to be with the "basename" function, which I wrote in fsfast. It may be that a function of that name already exists in your path and selxavg is not calling my function. You can try putting $FREESURFER_HOME/fsfast/toolb

Re: [Freesurfer] Seeing the Parcels as Volumes

Have you looked at aparc+aseg.mgz? You can change it to nii with mri_convert aparc+aseg.mgz aparc+aseg.nii On 8/27/18 5:54 AM, Maedeh Khalilian wrote: External Email - Use Caution Dear FreeSurfer experts, I have used "mri_annnotation2label" and "mri_label2vol" to change the parcella

Re: [Freesurfer] Using a cluster as an ROI for further analysis

First, run mris_preproc and mri_surf2surf commands as before to create a stack of P2 and P3. If you ran mri_glmfit-sim on P1,  then you will have an "ocn" output file. You can run mri_segstats --i P2P3.stack.mgh --seg ocn.mgh --id N --avgwf P2P3.means-in-clusterN.dat where N is the number of yo

Re: [Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 18696.1

The main problem is the 4th group where you only have two subjects and they are almost exactly the same age. This makes it hard to estimate the age slope and is causing the ill-conditioned error. You can try normalizing the ages (ie subtract the mean and divide by the stddev), you can remove ag

Re: [Freesurfer] T1 mapping

MA T: (617) 643-3869 *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve *Sent:* Friday, August 10, 2018 1:59:47 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] T1 mapping mri_fit_parms should do it. BTW, if you

Re: [Freesurfer] Plotting QDEC results

53 PM, Douglas Greve <mailto:dgr...@mgh.harvard.edu>> wrote: Each row is a subject and each column is a cluster. BTW, a threshold of 1.3 is way too low for lGI. If you want to use a threshold that low, you should use permutation instead of monte carlo (in general, permutation

Re: [Freesurfer] coregistering with bbregister

On 8/10/18 6:48 PM, Ben M wrote: External Email - Use Caution Hi Doug, Thank you for your suggestions, I'll try them. Could you please let me know if my code is actually doing what I intend it to do? Specifically, the idea is to perform functional-to-structural registration. so f

Re: [Freesurfer] Cortical surface

You can break up the aparc annotation into labels (mri_annotation2label), then create a new annotation with just the insula (mris_label2annot) On 8/12/18 5:17 AM, 郑凤莲 wrote: External Email - Use Caution Dear experts,   I an using FS 6.0 for cortical reconstructions.  I can show whol

Re: [Freesurfer] Surface Area in Toddlers/Children

is.edu <mailto:dandr...@ucdavis.edu> *From: * on behalf of Douglas Greve *Reply-To: *Freesurfer support list *Date: *Friday, August 10, 2018 at 10:25 AM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children It should be preserving total

Re: [Freesurfer] Confusion about MRI_GLMFIT

On 8/8/18 2:17 PM, Funk, Quentin wrote: External Email - Use Caution Freesurfer experts, I'm trying to figure out what values I get from mri_glmfit as in the tutorial. In particular, I'm interested in how I can c

Re: [Freesurfer] Correlations on QDEC

did you see the text where it says "If you seek help with this problem, make sure to send:" and then it gives a list of things to send? There will be a file called y.fsgd in the output, make sure to send that On 8/8/18 4:40 PM, Avi Gharehgazlou wrote: External Email - Use Caution Hi

Re: [Freesurfer] T1 mapping

mri_fit_parms should do it. BTW, if you are using a siemens scanner, you should just collect an MP2RAGE. That automatically outputs a quantitative T1 map using the two inversion technique. The results are much more accurate than using multiple flip angles On 8/8/18 5:00 PM, Fotiadis, Panagioti

Re: [Freesurfer] mri_volcluster not recognize --mindistance

Try --mindist not --mindistance On 8/9/18 9:08 AM, Yagmur Ozdemir 19 wrote: External Email - Use Caution Hello FreeSurfer experts, I am trying to run mri_volcluster with the following command to later create masks of clustered regions from functional data. I get an error saying that

Re: [Freesurfer] Plotting QDEC results

Each row is a subject and each column is a cluster. BTW, a threshold of 1.3 is way too low for lGI. If you want to use a threshold that low, you should use permutation instead of monte carlo (in general, permutation is better, but certainly for lGI). On 8/9/18 1:39 PM, Avi Gharehgazlou wrote:

Re: [Freesurfer] coregistering with bbregister

Sometimes the FSL initialization will fail. If you are using FS version 6, then run it without specifying --init-fsl and it will use mri_coreg, which is more robust. If your anatomical and functional were acquired at the same time, you might be able to get away with --init-header instead. On 8

Re: [Freesurfer] Viewing the output of mris_preproc in Freeview + export to Matlab

It is showing you the map of the first frame (subject in this case). You can adjust the frame with a slider on the left. Also, there is a time plot icon on the top. If you click on that it will show you a graph of the subjects at the chosen vertex. On 8/10/18 8:16 AM, Alon Baram wrote:  

Re: [Freesurfer] Surface Area in Toddlers/Children

It should be preserving total surface area. Can you send your mris_preproc command line and the terminal output? It might be something with 5.1 as well. On 8/9/18 3:49 PM, Derek Sayre Andrews wrote: External Email - Use Caution Dear Freesurfer Developers and Experts, I have been ex

Re: [Freesurfer] surface arithmetic?

Yea, just run mris_preproc on both subjects. There are even some options there for computing paired differences (simple differences or differences relative to the mean, etc) On 8/7/18 6:10 PM, Rockers, Elijah D. wrote: External Email - Use Caution Hello, I have a subject with two M

Re: [Freesurfer] Origin of freesusrfer output

s. Can you please tell, how can i get >>> back the first voxel of  input ? >>> Also, can you tell what mathematical formula or equation is used >>> convert this origin ? >>> >>> Thanks, >>> Ritesh Mahajan >>> >>> - Original Mess

Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics between groups analyses

I thought I answered this question last week. See my rsponse below I don't think it is correct conceptually.  By including SNR as a covariate, you are saying that you expect the thickness to increase with higher SNR and decrease with lower SNR. This does not make sense to me. It sounds like yo

Re: [Freesurfer] SNA covariate in cortical thickness between groups analysis

I don't think it is correct conceptually.  By including SNR as a covariate, you are saying that you expect the thickness to increase with higher SNR and decrease with lower SNR. This does not make sense to me. It sounds like you are trying to do a mixed effects analysis where you weight by the

Re: [Freesurfer] Origin of freesusrfer output

To add on, the origin is changed in that the "first voxel" is not the same in the 256^3 volume as it is in the original dicom. Having said that, all our files (eg, mgz and nifti) have a  matrix that converts a col, row, slice into the scanner RAS, so you can always find your way back to the dic

Re: [Freesurfer] no register.dat file for mri_label2vol

since you are mapping back into the conformed anatomical space, you should be able to use --identity instead of specifing a registration matrix On 7/26/18 8:25 PM, Ayzenberg, Vladislav wrote: External Email - Use Caution Greetings, I am trying to convert a surface label (e.g., lh.V1

Re: [Freesurfer] register mask to fsaverage

If the roi.nii does not include your areas of interest, then they will be masked out. The mask you create with mri_vol2surf may not be very accurate since it uses volume-based operation. On 7/26/18 5:19 PM, John Anderson wrote: External Email - Use Caution Dear Dr Greve, thank you so

Re: [Freesurfer] register mask to fsaverage

Don't use --regheader, use --reg $FREESURFER_HOME/average/mni152.register.dat On 7/26/18 4:40 PM, John Anderson wrote: External Email - Use Caution Dear Freesurfer experts, I have mask in MNI152 space. I would like to register this mask to fsaverage. How can I do this registration. I

Re: [Freesurfer] mri_glmfit

Use the mri.2mm aseg.mgz, eg,  mri_binarize --i aseg.mgz --match 7 8 46 47 --dilate 1 --o cblummask.mgz This will make a mask of cerebellum GM and WM and dilate it by 1 voxel. On 7/26/18 4:49 PM, Piero Chiacchiaretta wrote: External Email - Use Caution Dear FS group, I would like to re

Re: [Freesurfer] brain parenchymal fraction

you'll have to be more specific about what "brain surface contour" means. On 7/26/18 3:46 PM, Barletta, Valeria wrote: > Dear Freesurfers, > I need to extract the brain parenchymal fraction to check brain atrophy in my > patients. > The BPF is defined as "the ratio of brain parenchymal tissue vol

Re: [Freesurfer] converting a mask made in MNI space to subject space

Definitly do not use --rot 180. I think the registration matrix goes in the other direction, so try adding --inv to the command line and changing --targ and --mov On 7/25/18 8:24 PM, Sims, Sara A wrote: External Email - Use Caution Hello, I am trying to put a mask that I made on the

Re: [Freesurfer] ICV as covariate for controls vs. patients

especially, if it's always the case that for surface area and volume, we need ICV as covariate. On Thu, Jul 26, 2018 at 10:13 AM, Douglas Greve mailto:dgr...@mgh.harvard.edu>> wrote: If you are using surface area or volume, then you need ICV On 7/25/18 1:51 PM

Re: [Freesurfer] ICV as covariate for controls vs. patients

and without ICV as covariate. Clearly, adding ICV as covariate here, is reducing effect size all over the brain and without ICV effect size is higher at specific locations. So should I go ahead with or without ICV as covariate? Thanks. On Wed, Jul 25, 2018 at 7:33 AM, Douglas Greve <mailto:

Re: [Freesurfer] ICV as covariate for controls vs. patients

t method/way is the best and commonly used to confirm > these factors. > > Thanks. > > On Tue, Jul 24, 2018 at 7:06 AM, Douglas Greve mailto:dgr...@mgh.harvard.edu> > <mailto:dgr...@mgh.harvard.edu <mailto:

Re: [Freesurfer] Matched analysis with 2 controls 1 case weighting

On 7/24/18 1:56 PM, Dowling, Kevin Francis wrote: 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 th

Re: [Freesurfer] petsurfer

On 7/25/18 8:31 AM, John Anderson wrote: 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.

Re: [Freesurfer] tkregister2 scripting- help with saving reg.dat

no idea how to help with the vol2vol problem without a command line and more description of the problem On 7/24/18 6:52 AM, Yagmur Ozdemir 19 wrote: External Email - Use Caution By copying the matrix that comes up in the terminal, then readjusting it, if needed, in a different .dat f

Re: [Freesurfer] ICV as covariate for controls vs. patients

your results could have vanished after ICV correction for one of two reasons: the CV difference became less or the values became noisier (or a combination). So check in your data which one of those things happened. On 7/23/18 8:30 PM, Martin Juneja wrote: External Email - Use Caution

Re: [Freesurfer] Aparc.stats based on fsaverage?

The parcellation starts off in fsaverage space. It is mapped through the surface-based registration into the native subjects surface space. There, the boundaries are refined to better fit the individual. The transformation is based on folding patterns which are pretty consistent across the age

Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat

incorporate that into fcseedcor? Best, Hamdi *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve *Sent:* Friday, July 20, 2018 9:23:58 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer

Re: [Freesurfer] mri_binarize

It was just an oversight on my part when I wrote the program. I've just updated the file in our repository and put a copy here: https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize You can also specify all the structures you want by using the --match flag On 7/20/18 10:00 AM, John Ander

Re: [Freesurfer] Exporting results from QDEC

which results? On 7/20/18 9:11 AM, Avi Gharehgazlou wrote: External Email - Use Caution Hi experts, I want to make plots of my results that I have from QDEC, however, I'm having difficulty exporting values from QDEC. I examined LGI differences between groups, and I want to export my

Re: [Freesurfer] Bug in make_average_subject

where did you get the make_average_subject script? It is not the one that is released with version 6. On 7/20/18 3:46 AM, Raffington, Laurel wrote: External Email - Use Caution Dear Freesurfer Developers, My goal is to build a study-specific pediatric template brain to rerun the

Re: [Freesurfer] fcseedcor -- pca output for vcsf.dat and wm.dat

Hi Hamdi, sorry for the delay. Answers below. On 6/26/18 2:50 PM, Eryilmaz, H. Hamdi wrote: Hi Doug and Freesurfers, I am using fcseedcor to compute the correlation between two time courses for each subject in my group. The command that I run is as follows: fcseedcor -s $subject -fsd restin

Re: [Freesurfer] glmfit-sim FWHM 34?

can you send more info? command line, terminal output, what you are analuyzing, etc. If the fwhm is still 34, then something may be wrong. On 7/12/18 11:48 AM, Ting Li wrote: External Email - Use Caution Hi Douglas, I try to use permutation but it takes forever. I never see the end.

Re: [Freesurfer] Volumetric Group Analysis

The slicing (axial or otherwise) should not matter. But if the resolution (voxel size) is not good enough (~1mm), then you might get some blurry results. On 7/2/18 10:23 AM, Mr. Tass wrote: Good morning I hope everyone had a gr8 weekend. im new here so i hope someone can help me understa

Re: [Freesurfer] degrees of freedom

There are several questions here. First, the "optimal" design is to have an equal number in both groups. But this assumes that you have a fixed total number that you need to divide between the two groups. It is always better to have more subjects, even if the groups are not balanced in number

Re: [Freesurfer] TIV should be considered as a covariant for thickness, volume and area analyses

Yes, for area and volume, no for thickness On 6/29/18 3:06 PM, Ting Li wrote: > External Email - Use Caution > > Hi FreeSurfer Experts, > > I would like to do the surface analysis among two groups, like the thickness, > volume and area. When I run the GLM, do I have to consider the eTIV

Re: [Freesurfer] mri_glmfit question

You can create a surface overlay in matlab and display it using freeview.  See https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m To read it into matlab, you can run pcc = MRIread('pcc.mgh'); You can convert it to text with mri_convert --ascii pcc.mgh outputtextfile On 6/2

Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

un 25, 2018 at 10:14 AM, Douglas Greve mailto:dgr...@mgh.harvard.edu>> wrote:       It should be included. But dACC and insula are not close to each other. How can       there be a cluster that spans both?       On 6/23/18 7:54 PM, srishti goel wrote:

Re: [Freesurfer] Question about GLM results in Freesurfer

  --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_FFMQ_f1.mtx \   --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_FFMQ_f2.mtx \   --surf fsaverage lh Message: 4 Date: Mon, 25 Jun 2018 10:45:42 -0400 From: Douglas Greve mailto:dgr...@mgh.harvard.edu>> Subject: Re:

Re: [Freesurfer] Using T2 or Flair data to improve pial surfaces

, Madison WI 53705  608-219-4294 | hlindr...@wisc.edu *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve *Sent:* Tuesday, June 19, 2018 9:38:25 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re

Re: [Freesurfer] Question about GLM results in Freesurfer

Are you doing 5 different tests or just one test? It is a tricky question as to whether you should correct across  5 tests or not. Ideally, one should, but I don't think I've ever seen it done in practice. As a reviewer, I might not demand it for only 5 tests. On 6/20/18 9:17 AM, jahanvi pat

Re: [Freesurfer] Group Analysis Covariates

sorry for the delay. There is not a super easy way to do this, but it is possible in matlab. cd into the glmdir folder and start matlab, then X = load('Xg.dat'); beta = MRIread('beta.mgh'); betamat = fast_vol2mat(beta); yhatmat = X(:,[i j k m n])*betamat([i j k m n],:); yhat = beta; yhat.vo

Re: [Freesurfer] mri_vol2surf: dACC/Insula clusters on surface not found

It should be included. But dACC and insula are not close to each other. How can there be a cluster that spans both? On 6/23/18 7:54 PM, srishti goel wrote: External Email - Use Caution Hello, I am using mri_vol2surf to project my volume maps on to the surface. There is a dACC/insul

Re: [Freesurfer] Using T2 or Flair data to improve pial surfaces

Did you run recon-all with -qcache ? On 6/19/18 9:30 AM, Heidi Lindroth wrote: External Email - Use Caution Hi there, I have used T2/Flair images to improve the pial surface reconstruction, however, when I tried to analyze these data in QDEC, I was unable to load the files because

Re: [Freesurfer] mri_gtmpvc

Yes, if you  set  --psf 0 then it will only apply correction for the tissue fraction effect (TFE). On 6/15/18 10:53 AM, Alshikho, Mohamad J. wrote: Dear Dr Greve, Kindly, I’d like t to inquire about the command “mri_gtmpvc” in PET surfer. Can I use this command to apply partial volume corre

Re: [Freesurfer] TotalGrayVol and SubCortGrayVol for multiple subjects

It should auotmatically be included in the output asegstats2table. is it not? On 6/15/18 10:23 AM, Fernanda Hansen P. de Moraes wrote: External Email - Use Caution Good morning all, I want to get the TotalGrayVol and SubCortGrayVol for multiple subjects. Is there any flag that I ca

Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas

There are files called lh.area and lh.volume that you can use instead of lh.thickness. Make sure to use the --jac flag when applying mri_surf2surf to area or volume (but not thickness). This applies jacobian correction to preserve the total area or volume. When you run mri_segstats, include the

Re: [Freesurfer] [Request of response] Fwd: Error during QDEC

Those are the qdec tables, not the fsgd file. Look in the qdec output folder for a file called y.fsgd. Also please remember to post to the list and not to us personally On 6/15/18 12:40 AM, Seung-Gul Kang (강승걸) wrote: External Email - Use Caution Hi Doug, Thank you for your reply.

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