Re: [Freesurfer] resample_type ignored by mri_convert with --like argument?

try this mri_vol2vol --targ T1w_MNI.nii.gz  --interp nearest --mov ICBM152_2009c_AtlasWhite.nii.gz   --o WhiteAtlas_resampled.nii.gz On 5/9/2022 11:58 AM, James Hengenius wrote: External Email - Use Caution Hello FS experts, I'm trying to reslice a third-party atlas into the same r

Re: [Freesurfer] [External] Re: Reversing mri_convert

-- *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursday, May 5, 2022 4:36 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] Reversing mri_convert What does "isn't displaying the same i/j/k ras"

Re: [Freesurfer] Recon-all

On 5/5/2022 9:53 PM, krystaly wrote: External Email - Use Caution Dear Freesurfer experts, I am new to FS 7.2.0 (Window 10), and trying to run the Recon-all command as demonstrated on the website (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claimi

Re: [Freesurfer] error estimates in FS total brain volumes

Can you clarify what you mean by margin of error? What are you looking for? On 5/5/2022 6:10 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi all, What is a reasonable estimate of the error margin in the total brain volume estimates of Freesurfer? Is there a refere

Re: [Freesurfer] DT_recon error

There might be something wrong with the dicom, so first, try to convert the dicom to nii.gz with mri_convert On 5/10/2022 3:23 AM, m-maiw...@web.de wrote: External Email - Use Caution Hi all, I try to run dt_recon on my dicom files, acquired with a siemens scanner unsing the command

Re: [Freesurfer] Curvature data question

qlq-yVRqSuWcM9qireeQDFjj4%2Fview%3Fusp%3Ddrive_web> On Tue, Apr 26, 2022 at 2:07 PM Douglas N. Greve wrote: sorry, just looking at it now. Can you send the 1mm results as well? On 4/25/2022 7:42 PM, Samuel Paré wrote: External Email - Use C

Re: [Freesurfer] Reversing mri_convert

What does "isn't displaying the same i/j/k ras" mean? In what tool? What is the result of running mri_info on each volume? On 5/5/2022 4:54 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution For some reason it isn't displaying the same i/j/k ras. The

Re: [Freesurfer] recon-all -long error (the third step of the longitudinal pipeline)

What happens if you remove -parallel? That flag does not do much any more but cause trouble (we have removed it in recent versions) On 5/3/2022 2:58 PM, FONG, manson CM [CBS] wrote: External Email - Use Caution Hello Experts, I'm attempting to run the longitudinal pipeline, as descri

Re: [Freesurfer] mri_surf2surf error

what happens if you run mri_info lh.CCn_band.Seed1_20220314.V1.13subjs.mgh On 5/3/2022 11:54 AM, Zhang, Fan wrote: External Email - Use Caution Hello Everyone, I am trying to run mri_surf2surf. But I got some errors saying "no such file or directory" while in fact there are files in

Re: [Freesurfer] segmentHA_T1, mri_segstats: How can I get the PVC uptake for amygdalar nuclei?

I don't think it is a good idea to try to PVC the amygdalar segmentations as they are too small. On 4/28/2022 4:27 PM, Tun, Samantha wrote: External Email - Use Caution Hello Freesurfer Devs! I am attempting to extract the tau uptake in the amygdalar segmentations. I ran this comman

Re: [Freesurfer] Curvature data question

qlq-yVRqSuWcM9qireeQDFjj4%2Fview%3Fusp%3Ddrive_web> On Tue, Apr 26, 2022 at 2:07 PM Douglas N. Greve wrote: sorry, just looking at it now. Can you send the 1mm results as well? On 4/25/2022 7:42 PM, Samuel Paré wrote: External Email - Use Caution

Re: [Freesurfer] Scalable recon workflow

btw, it will almost certainly be more efficient to run each subject with 1 thread and run them all at the same time rather than running a few of them with 4 or 8. If you can run them all with multiple threads, then that might be more efficient (depends on your scheduler, for slurm it would be).

Re: [Freesurfer] Permission denied error from -localGI

ine 25) volume=vol.vol; >> ERROR: make_outer_surface did not create output file What can we do now? -Tashrif     ===     Douglas N. Greve Wed, 27 Apr 2022 07:51:33 -0700     Can you just try it with 7.2? We had some problems at one point with temporary files in lGI tha

Re: [Freesurfer] Average subject and head size

It will remain in talairach space ( actually mni305) On 5/2/2022 1:08 PM, Sébastien Daligault wrote: > External Email - Use Caution > > Hi support, > I have a naive question about the make_average_subject function. > I want to average MRIs to create a template. > This process uses the ta

Re: [Freesurfer] error for qdec

qdec has been retired and is not available in 7.2.0 On 5/2/2022 10:30 AM, Chen ZY wrote: External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to use qdec tool, but I received the following error when I type qdec in the terminal: developer@developer-VirtualBox:/us

Re: [Freesurfer] Resampling of surface-based bivariate data

You'd have do both the rows and the cols. On 4/27/2022 11:44 AM, Fischl, Bruce wrote: > Why not just flatten it and save it as a .mgz? Then I think it should be > straightforward > > -Original Message- > From: Greve, Douglas N.,Ph.D. > Sent: Wednesday, April 27, 2022 10:42 AM > To: frees

Re: [Freesurfer] Permission denied error from -localGI

     Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700 === What version of FS are you running? On 3/20/2022 8:47 PM, Billah, Tashrif wrote:     It does not exist and cannot be created in a shared cluster. Is there a way to define a different folder for

Re: [Freesurfer] Beta values (resubmitting)

k you so much, Laura. *De:* Douglas N. Greve *Enviado:* terça-feira, 26 de abril de 2022 15:01 *Para:* Laura Willers de Souza *Cc:* freesurfer@nmr.mgh.harvard.edu *Assunto:* Re: [Freesurfer] Beta values (resubmitting) 3rd lin

Re: [Freesurfer] Resampling of surface-based bivariate data

No, there is not (at least that I know of). Bruce might have something along these lines. On 4/26/2022 3:32 PM, Burke Rosen wrote: > External Email - Use Caution > > Is there a way to resample a vertex-by-vertex matrix of data from one subject > to another or to ico? For example, I have

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

yes, in the gtm.stats file. See https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer for docs On 4/26/2022 3:29 PM, Zhener Zhang wrote: External Email - Use Caution Thank you, Douglas! Is it possible to extract the number of voxels in each segment [of the FreeSurfer DK atlas]? We are

Re: [Freesurfer] Beta values (resubmitting)

3rd line for the slope of CU, 4th line for the slope of CI On 4/25/2022 4:03 PM, Laura Willers de Souza wrote: External Email - Use Caution Thanks so much! I would also like to confirm that I am interpreting the beta values correctly for a second model. Model 2: Two Groups, One Cov

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

In that case, it mapping the seg into the pet space (see aux/seg.nii.gz) and just averaging over the voxels in each segment. On 4/25/2022 2:34 PM, Zhener Zhang wrote: External Email - Use Caution Hi Douglas, Thanks! We ran the following for one of our subjects: mri_gtmpvc --i sz

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

There are several ways it might work depending upon how you ran it. This is why I was asking for your command line. On 4/24/2022 4:46 PM, Zhener Zhang wrote: External Email - Use Caution Hi Douglas, Thank you for the reply! The mri_gtmpvc outputs were expected and there was no reaso

Re: [Freesurfer] ERROR: Talairach failed!

*Von:* freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve *Gesendet:* Donnerstag, 21. April 2022 20:03:32 *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] ERROR: Talairach failed! Can you provide the tkregisterfv command line

Re: [Freesurfer] mri_segment_hypothalamic_subunits error

From Benjamin Billot: Yep, that’s just an out of memory issue for the GPU. He/she can use the cropping flag, or use the cpu flag. On 4/18/2022 9:58 AM, Chen ZY wrote: External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to use the mri_segment_hypothalamic_subunit

Re: [Freesurfer] ERROR: Talairach failed!

Can you provide the tkregisterfv command line and the terminal output? On 4/21/2022 3:37 AM, Fritze, Stefan wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to computerecon-all -all -subjid XXX -qcache -3T, which works fine with most of my study partici

Re: [Freesurfer] differences between Freesurfer 6.0 and 6.0-beta

basically, you should not have been using the beta version since it is a beta version. hard to know what the differences were On 4/20/2022 6:21 PM, Paul Wighton wrote: External Email - Use Caution Hi Matt, freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c was compiled from t

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

Can you send your mri_gtmpvc command line? On 4/20/2022 12:50 PM, Zhener Zhang wrote: External Email - Use Caution Hello, I have a question regarding the way ROI-wise values are calculated using PETSurfer. We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively smal

Re: [Freesurfer] recontruction of an elephant brain

g foward, Malav Shah -------- *From: *"Douglas N. Greve" *To: *"freesurfer" *Sent: *Saturday, April 9, 2022 10:18:18 PM *Subject: *Re: [Freesurfer] recontruction of an elephant brain Lot's of people have adapted FS to non-human brains, just google it. For surface analysis,

Re: [Freesurfer] rerunning on 7.2 with edited brainmask using hi-res

Yes, same command On 4/17/2022 10:24 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Can someone confirm? Thx. Jim *From:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Alexopoulos, Dimitrios *Sent:* Tuesday, April 12, 2022 3:24 PM *To:* Freesurfer support

Re: [Freesurfer] Recon process for skull-stripted data

I'm not sure. You can try just passing the skull stripped as input to recon-all. The talairach transform will probably be off, but the rest might work On 4/17/2022 9:09 PM, Muhammed Görünen wrote: External Email - Use Caution Hi, How can I run a recon process if I have just skull st

Re: [Freesurfer] Rerunning freesurfer with manual edits and T2 or FLAIR pial refinement

you need to add these flags again On 4/16/2022 11:49 AM, VINCENT KOPPELMANS wrote: External Email - Use Caution I have made manual edits to a subject that was initially run with the -FLAIR and -FLAIRpial input flags. When I want to rerun freesurfer to implement these edits should I

Re: [Freesurfer] Multiple comparison correction

Do you mean the difference between the d,m,h classes? If so, it would be 1 1 -1 -1 0 0 (rest all 0s) 1 1  0  0 -1 -1 ... 0 0 1 1 -1 -1 ... On 4/14/2022 9:50 AM, David wrote: External Email - Use Caution Hi Freesurfer experts,     I'm very sorry to bother you, but I am very confused

Re: [Freesurfer] How to make surfaces below the GM-WM boundary?

Try using mris_expand, eg, mris_expand lh.white -1 lh.subwhite will create a surface 1mm into the WM On 4/14/2022 7:50 AM, Lee Subin Kristine wrote: External Email - Use Caution Dear FreeSurfers, I am interested in sampling values in the superficial white matter (SWM) region, which i

Re: [Freesurfer] [Freeview] View Flatmap

in freeview, runsomethiing like freeview -f rh.white:patch=rh.full.flat.patch.3d The rh.white is just there to give freeview a full surfce to load. You will only see your patch On 4/14/2022 4:30 AM, Morgenroth Elenor wrote: External Email - Use Caution Dear Freesurfer Experts, I have

Re: [Freesurfer] Beta values (resubmitting)

Yes, first line intercept, 2nd line slope On 4/12/2022 3:44 PM, Laura Willers de Souza wrote: External Email - Use Caution Hey! I'm resending this email because I think it got lost on the list. Hello FreeSurfer Developers, I'm extracting beta values​​from some analyzes and I would li

Re: [Freesurfer] parallel make_average_subject

There is not an easy way to do this. Internally, there is a binary that loads all the subjects then creates an average. You need some way to create intermediate files, then combine them together, which we don't support. Why do you want to create an average subject? On 4/11/2022 9:54 AM, Marina

Re: [Freesurfer] mri_glmfit error

You don't have enough members in the classes to fit the model that you have. Eg, class d has 4 members with which you are fitting an offset and 3 slopes leaving you with 0 degrees of freedom. You need to get more subjects or change your model. btw, gender is usually modeled as a discrete rather

Re: [Freesurfer] mkheadsurf error: mris_smooth and mris_inflate synthesized bizarre output paths

10 -sulc /... resulting in error: MRISwriteCurvature: could not open /... Lastly, I followed the response from Douglas N. Greve <https://secure-web.cisco.com/1ahbUvtJEJ2YIzAb-v2Vq6dQ8vxhI4tzwwkf_H3Yz4GyLGM7YvV79qByQvW-Kpj0lueIrI67DwfRrcgmTtD9jyK7SHOSxPScms3rWbYgKXx0gVxlWTJGfbgLxIY60CqFq6wtKL

Re: [Freesurfer] Freesurfer stats output meaning

wow, I've never even looked at the ?h.curv files before. Looks like there is a lot of info but only on a global (whole hemi basis). Some of the measures are different (eg, min and max curv rather then mean or gaussian). I don't know whether these would be helpful in your app. On 4/5/2022 12:16

Re: [Freesurfer] Medial prefrontal cortex

one i cant find in there ( perhaps there is a different name for the medial frontal gyrus in the a2009s). Thank you again in advance for your help. Best wishes, Patricia Le lun. 4 avr. 2022 à 03:55, Douglas N. Greve a écrit : Have you looked in the destrieux atlas? It is the a2009s anno

Re: [Freesurfer] recontruction of an elephant brain

Lot's of people have adapted FS to non-human brains, just google it. For surface analysis, you need to get the "subcortical mass" -- the equivalent to the filled.mgz. This is the cerebral white matter + subcort gray structures. Once you have that, you might be able to run mris_place_surfaces. I

Re: [Freesurfer] recon-all error in a specific data

Did you check the transform? It was the automatic failure detection that threw the error. This can sometimes happen when the head is at a "funny" orientation in the scanner, but at 7T there might be some bias fields having an effect. Also, see if it works when you sample it at 1mm (just don't u

Re: [Freesurfer] DenoiseImage shifting scan orientation

have you tried asking the ANTS people? On 4/6/2022 10:05 AM, Nathan Kindred (PGR) wrote: External Email - Use Caution Hi, I have been using DenoiseImage from ANTs during pre-processing (DenoiseImage -i T1.nii -o denoised.nii.gz -v), however for some scans I am having an issue where

Re: [Freesurfer] Inverse transform

The rawavg.mgz should be the same dimension as your T1 MPRAGE. Why are they not? Look at the dims for the  volume subject/mri/orig/001.mgz On 4/4/2022 2:25 AM, Aleksandra Szum-Jakubowska wrote: External Email - Use Caution Dear Freesurfer Experts, I conduct the segmentations' examines

Re: [Freesurfer] Tkregister2 not opening GUI

S0727" "S0738") recon-all -autorecon1 -subjid "$i"_FS end *From: *freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Date: *Monday, April 4, 2022 at 10:56 *To: *freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Tkregister2 not op

Re: [Freesurfer] Tkregister2 not opening GUI

*From: *freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Date: *Sunday, March 27, 2022 at 16:59 *To: *freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Tkregister2 not opening GUI *CAUTION:* This email originated from outside of Georgian College. Do not click links or op

Re: [Freesurfer] slice timing for multiband fMRI

You can give mkanalysis-sess the slice order with -stc as you would with an ordinary non-accellerated scan. Then give it the number of slice groups with -ngroups nSliceGroups I don't quite remember what nSliceGroups means, but I think it means the number of simultaneously acquired slices. On 3/

Re: [Freesurfer] Questions regarding ROI creation for SPM based on FreeSurfer parcellation

I would probably just use the 1st option. On 3/30/2022 5:20 AM, Falko Mecklenbrauck wrote: External Email - Use Caution Dear FreeSurfer-Experts, I’m in need of your experience to help me with a decision in my current project: I want to use certain areas, that were identified by str

Re: [Freesurfer] mri_vol2vol anatomical to functional

Have you visually verified that the registration is correct (only work with LTAs) using tkregisterfv ? How are you viewing the combined anatomical/functional in pics? If you just load the functional without a registration file, then that is not right. On 3/29/2022 11:28 AM, Manenti, Giorgio wr

Re: [Freesurfer] lh.white surface co-registration

he new ones as well? It is just the thickness values at each point. They xyz is implicitly associated with the point. I appreciate your time and help as always. Ela _________ Fr

Re: [Freesurfer] repeated measures ANOVA 2x2 covariate

? How can I calculate the difference between the two time points? Thank you very much. Best regards, Agurne El dom, 27 mar 2022 a las 23:07, Douglas N. Greve () escribió: Probably the easiest thing to do since you have only two time points is to compute the difference between the

Re: [Freesurfer] Beta values

Can you send the fsgd file? On 4/1/2022 3:28 PM, Laura Willers de Souza wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm extracting beta values ​​from some analyzes and I would like to know if I'm extracting and interpreting these values ​​correctly. To extract

Re: [Freesurfer] Medial prefrontal cortex

Have you looked in the destrieux atlas? It is the a2009s annot. On 4/1/2022 10:28 AM, Patricia Schwery wrote: External Email - Use Caution Hi there, I would like to know if someone could tell me how i can measure the medial prefrontal cortex (mPFC) with freesurfer as i see it is di

Re: [Freesurfer] transitioning from tkmedit to freeview

Note also that  you can use tkmeditfv to run freeview with tkmedit-like options (and more). On 3/30/2022 8:00 PM, Wang, Ruopeng wrote: Hi Victor, On Mar 30, 2022, at 4:30 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution Hi, My lab has been usin

Re: [Freesurfer] GLM analysis - volume and surface area

n the correction of multiple comparisons. Many thanks! -- On 3/09/2022 15:20 PM, Douglas N. Greve wrote: Can you just ask the question again so I don't have to sort it

Re: [Freesurfer] WM error near the right putamen

This is actually a bug in version 7.[012]. This area is probably not valid anyway. We'll have a fix in 7.3 On 3/21/2022 7:31 PM, Gabor Perlaki wrote: External Email - Use Caution Dear all, fswiki suggests that " There are regions where the surfaces are not intended to be accurate th

Re: [Freesurfer] lh.pial and rh.pial is 0Kb, I cannot open them by using freesurfer

On 3/24/2022 4:49 PM, Muhammed Görünen wrote: External Email - Use Caution Hi, I run recon-all process for a subject's T1 data. At the end, the pial files are 0Kb and I cannot open them from python. Did it end with an error? Did you run out of space? What version of FS? Can you sen

Re: [Freesurfer] [External] Re: [External] Re: classes for GLM analysis

stat_fwep.mgz" This is with Freesurfer dev 20211206. Thanks and sorry for so many questions lately Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- *From:* freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Question about calculation of pial area in DKatlas

On 3/24/2022 2:53 AM, Dongyue Zhou wrote: External Email - Use Caution Dear FreeSurfer experts: I want to calculate mean pial surface area in DKatlas in individual space.And I know the function read_annotation.m in $FREESURFER_HOME/matlab for loading this atlas. And if I ca

Re: [Freesurfer] mri_vol2vol anatomical to functional

I'm not sure I understand what you are saying or what the problem is. Can you provide the actual command line you are using, all the terminal output, and a picture that shows what the problem is? On 3/23/2022 2:46 PM, Manenti, Giorgio wrote: > External Email - Use Caution > > Dear Frees

Re: [Freesurfer] mri_segment_hypothalamic_subunits error: Illegal instruction 4

You're command line is incomplete (it needs more than just --s). Run it with --help and/or visit the wiki page On 3/23/2022 2:40 PM, Alice Tao wrote: External Email - Use Caution Thank you so much for the response! Unfortunately, that is the full command line and output: $ mri_segm

Re: [Freesurfer] repeated measures ANOVA 2x2 covariate

Probably the easiest thing to do since you have only two time points is to compute the difference between the two, then just do a simple group analysis where you include the covariates that you want. On 3/23/2022 10:00 AM, Agurne Sampedro Calvete wrote: External Email - Use Caution D

Re: [Freesurfer] qdec analysis error

Sorry, we are not supporting qdec anymore. You will need to use the command-line stream On 3/23/2022 8:02 AM, David wrote: External Email - Use Caution Hello FreeSurfer Developers, I have a problem. Can you help me freesurfer version : 6.0.0 Load qdec when I run qdec.table.dat, the

Re: [Freesurfer] Negative eTIV

Check the talairach registration (talairch.xfm). It must be badly messed up On 3/23/2022 4:47 AM, lqcheng2017 wrote: External Email - Use Caution Dear experts, I extracted the eTIV using the mri_segstats, but it showed negative value. How could I solve this problem? Thank you very

Re: [Freesurfer] Freesurfer mri_convert

please send the command line, log file, version of FS, etc On 3/22/2022 11:59 AM, Zoe O'Brien-Moran wrote: External Email - Use Caution Dear FS Experts I am having continued issues with the mri_normalize function on MPRAGE data I get an error message: 3d normalization pass 1 of 2 e

Re: [Freesurfer] Tkregister2 not opening GUI

;S0524" "S0525" "S0528" "S0537" "S0544" "S0557" "S0589" "S0601" "S0650" "S0669" "S0676" "S0682" "S0715" "S0727" "S0738" "S0741" "S0747"

Re: [Freesurfer] Permission denied error from -localGI

What version of FS are you running? On 3/20/2022 8:47 PM, Billah, Tashrif wrote: It does not exist and cannot be created in a shared cluster. Is there a way to define a different folder for /scratch/tp24093955057547375.load_mgh.m.mgh? === Douglas N. Greve Wed, 09 Mar 2022 10:04

Re: [Freesurfer] vertexwise correlation between the two maps and atlases in volume (MNI) to surface

On 3/17/2022 4:41 PM, std...@virgilio.it wrote: External Email - Use Caution Hi list, a) I have two maps, one's of rs-fMRI functional connectivity (by FS-FAST) and one's of receptor density (from a PET-Atlas). Both the maps are in surface space. How can I measure the vertexwise co

Re: [Freesurfer] Turning Significant Cluster (sig.cluster.summary or sig.mgh) into binary .nii ROI

Are you trying to create a volume-based binary mask or a surface-based mask? From the commands below, it looks like surface (but why would you need it to be in nii?). In the surface case, you can just mri_binarize --i ocn.mgh --match clusterno --o clusterno.mask.nii where "ocn" is the ocn file c

Re: [Freesurfer] Tkregister2 not opening GUI

Can you try tkregisterfv ? The old tk tools are not supported any more. tkregisterfv uses freeview On 3/17/2022 6:03 AM, Nathan Kindred (PGR) wrote: External Email - Use Caution Hi Isabelle, It’s been a couple of years since I ran FreeSurfer on a Mac, but I also have had this issue

Re: [Freesurfer] lh.white surface co-registration

If you have an LTA file, you can run mris_apply_reg --lta lh.white your.lta lh.white.newcoords On 3/16/2022 4:15 PM, Salar Dini, Elaheh wrote: External Email - Use Caution Dear Freesurfer experts, Is there a way to move lh.white of a subject to a new coordinate? Something quite simil

Re: [Freesurfer] recon-all errors after mri_pretess

spot.  The log is attached. Jim *From:*freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Wednesday, March 09, 2022 12:24 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] recon-all errors after mri_pretess ** External Email - Caution ** Does this

Re: [Freesurfer] Using vol2surf to fsaverage.

Yes, just specify --regheader subjectname instead of a --reg On 3/11/2022 9:34 AM, Jacoby, John wrote: Hi all, Usually when I want to map volume data to the fsaverage surface, I use mri_vol2surf with a registration that transforms the volume into the space of the subject's orig.mgz and with -

Re: [Freesurfer] FWHM errors for mri_glmfit-sim for lgi?

Yes, oftentimes. You should not smooth the LGI. Also, I would strongly suggest that you use permutation instead of mcz sim. For perm, the fwhm won't matter. On 3/10/2022 3:26 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: External Email - Use Caution I receive FWHM values mu

Re: [Freesurfer] how to load flat surface in freeview

What happens if you run freeview -f /home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.inflated On 3/10/2022 7:32 AM, Francesca Strappini wrote: External Email - Use Caution Dear Freesurfer experts, I'm trying to load the flat surface that I created with this command line: m

Re: [Freesurfer] Atlas of primary motor and auditory cortex

On 3/9/2022 2:15 PM, Jingyi Wang wrote: External Email - Use Caution Hello Freesurfer experts, I ran the recon-all command and got all the .label files for the segmentations of the cortical areas. However, I have some questions about the label for primary motor and auditory cortex.

Re: [Freesurfer] complete unfinished steps of recon all

Yea, not so easy. You need to see how far it got and then use the appropriate flags. The most time consuming step is the volume labeling. See if aseg.presurf.mgz exists. If it does, then you can skip that with -autorecon2-noaseg -autorecon3. If subject/mri/transforms.m3z and norm.mgz exist but

Re: [Freesurfer] [External] Re: classes for GLM analysis

aren't treated like integers Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Sunday, February 13, 2022 12:24

Re: [Freesurfer] Cutting the Full Surface

In FreeView Click on the brain with scissors icon ("Cut"), select your points, then "Cut Closed Line",    make sure the cusror is in the patch, then hit "Fill Uncut Area", then save as a patch On 3/7/2022 12:03 PM, Francesca Strappini wrote: External Email - Use Caution Dear FreeSu

Re: [Freesurfer] recon-all errors after mri_pretess

Does this fail every time like this? It looks like it just abruptly stopped. Does anything print out to standard error? On 3/4/2022 11:18 AM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi, we’re running FS 7.2 ‘recon-all -all’ on a subject and are getting errors on ou

Re: [Freesurfer] Using T1 FLAWS in recon-all

never heard of FLAWS. My good search says that it is WM and CSF suppression, so it probably won't work. On 3/4/2022 6:10 AM, Mathilde Pichon wrote: External Email - Use Caution Hello, I know T1 MPRAGE is the prefered format to perform a recon-all segmentation. But some of my patien

Re: [Freesurfer] ERROR: Flag -sveres unrecognized

What version are you trying to run? selxavg-sess has been depricated for years. Try selxavg3-sess On 3/3/2022 10:59 AM, CALLACHAND Muntasir wrote: External Email - Use Caution Hi, I have a problem when i try to run the function selxavg-sess

Re: [Freesurfer] Error: inputs cannot have multiple frames

It means that you have two frames in the 001.mgz file. Sometimes this happens with multiecho mprages. If this  is the case, you can convert your input to a single frame with mri_concat --rms file.mgz --o file.rms.mgz Then use file.rms.mgz as the input to recon-all On 3/3/2022 12:04 AM, HYE JUNG

Re: [Freesurfer] bbregister dependencies recon-all

You pretty much have to run it through to the end. You can try using mri_coreg (this is the first step of bbregister). It does not need anything but two images and will  run in  a few min. On 3/3/2022 5:24 AM, Guillem París wrote: > External Email - Use Caution > > Hello, > > I'm trying

Re: [Freesurfer] GLM analysis - volume and surface area

n of multiple comparisons. -- On 2/21/2022 15:20 PM, Douglas N. Greve wrote: Yes, it is. It is confusing when you talk about area and volume sincethese are not point measures like thickness (ie, what is the volume orarea of a vertex?). The area of a

Re: [Freesurfer] Permission denied error from -localGI

Do you have permission to /scratch? Does it exist? On 3/2/2022 9:50 AM, Billah, Tashrif wrote: Hi all, We are trying to run recon-all with -localGI but running into an unknown permission denied error: $ recon-all -s sub-1001 -localGI ``` make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-100

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

ive%2Ffolders%2F1QNzMxJdmc7Bo1KGlh9OC9f7DVzZ9ej2k%3Fusp%3Dsharing> Thank you in advance, Hyunwoo Jeong. 2022년 2월 26일 (토) 오전 8:16, Douglas N. Greve 님이 작성: Can you upload the data to me somewhere? I'd need the input volume and the fsgd and any contrasts On 2/21/202

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

o you have any other suggestions? I appreciate your help so far. Best, Hyunwoo Jeong 2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve 님이 작성: It looks like it is failing when computing the partial correlation coef. Try  running it with --no-pcc On 2/16/2022 10:53 AM

Re: [Freesurfer] Using mri_transform with output of bbregister

This is a bit tricky as you need a volume as a template that has the dimensions/resolution you want. One fast and dirty way to do it is to upsample the orig to 0.5mm, eg mri_convert --upsample 2 orig.mgz orig.us2.mgz You can then run mri_vol2vol --mov T2.nii.gz --lta reg.lta --targ orig.us2.mgz -

Re: [Freesurfer] Neverending mris_fix_topology

You can't tell from the image whether the wm in cerebellum or dura is attached. you need to look at the wm.mgz volume to see. You can load the ?h.orig.nofix as well. In the terminal output of recon-all/topofix, it should give a vertex number of the topodefect. Go to that vertex n the nofix surf

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

rom: * on behalf of "Douglas N. Greve" *Reply-To: *Freesurfer support list *Date: *Friday, February 25, 2022 at 10:25 AM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis Are you doing an ROI analysis or a v

Re: [Freesurfer] Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames!

I'm not sure what question you are asking On 2/25/2022 1:17 PM, Knut J Bjuland wrote: External Email - Use Caution DearFreesurferexperts, IgetthiserrorwhenIamrunning FreeSurfer. Checkingfor(invalid)multi-frameinputs... ERROR:input(s)cannothavemultipleframes! /home/knutjb/subjects/t

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

behalf of "Douglas N. Greve" *Reply-To: *Freesurfer support list *Date: *Tuesday, February 22, 2022 at 3:00 PM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis I don't understand. What mask? On 2/22/2

Re: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter

am: just generally interested. For my work, I am > looking at ventricular volume and so it would be good to not have to manually > correct a large number of my scans. > > From: Douglas N. Greve > Sent: Tuesday, January 4, 2022 1:19 PM > To: freesur

Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics

r descriptions. Thanks, Alex *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Tuesday, February 22, 2022 5:20:45 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-proc

Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

Douglas N. Greve *Sent:* Monday, February 21, 2022 6:29 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness I just updated the code to accept PVRs. I'm not sure what I have to do to test it; I guess I need t

Re: [Freesurfer] Annotation File to ROI Volume Estimate

I see it in the help:    -b     tabular output On 2/24/2022 12:23 PM, Jacoby, John wrote: Hi Doug, thanks for the pointer. That was exactly what I was looking for. When I copied the command from recon-all.log, it used a -b flag. I can't find documentation for this flag either

Re: [Freesurfer] Dividing surface overlays

You can also look in pctsurfcon. This compute the percent gray/white contrast. It does so on the T1w, but you could look inside the script to see how it does it and adapt to your situation. On 2/23/2022 3:26 PM, Adam Martersteck wrote: External Email - Use Caution Hi Dylan, Give thi

Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics

ancke Drive Columbia, MO 65211 Contact: 573-884-8779 *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Monday, February 21, 2022 9:21 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject

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