Re: [Freesurfer] Questions about contrasts

razil __ Answer by Douglas N. Greve: Hello FreeSurfer Developers, I want to perform an analysis of the difference between two groups incortical thickness, having cor

Re: [Freesurfer] Questions about contrasts

Can you include the previous emails in your current email? On 12/14/2021 3:46 PM, Laura Willers de Souza wrote: External Email - Use Caution Dear Douglas, Thank you so much for your answer! Sorry, but I don't think I explained myself correctly in the previous email. I want to anal

Re: [Freesurfer] Help

me instructions on how to fix these defects? Thanks, Nilab ---- *From:* Douglas N. Greve *Sent:* 11 December 2021 00:24 *To:* Nilab Nasrullah ; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Help The data look

Re: [Freesurfer] Doubts about analysis of hippocampal subfields and nuclei of the amygdala

use the asegstats2table command in https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala You will have to add command line options to specify the subjects you want. You can then pass the output file with the --table option to mri_glmfit On 12/13/2021 3:56 PM, Laura

Re: [Freesurfer] Questions about contrasts

The model is actually, two independent linear models: thicknessCU = CUOffset + CUcortisol*CUslope thicknessCI = CIOffset + CIcortisol*CIslope There will be four regression parameters: [CUOffset  CUslope CIOffset CIslope] On 12/9/2021 10:48 PM, Laura Willers de Souza wrote: External Em

Re: [Freesurfer] Error: recon-all exited with ERRORS: failing without generating all surf files: How to modify wm.mgz to make it work?

In that case, you should edits the wm.mgz (first web page) to find the big defect. There are not any surfaces at this point because it did not get that far On 12/9/2021 3:53 AM, Sumit Sharma wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to generate

Re: [Freesurfer] Doubts about analysis of hippocampal subfields and nuclei of the amygdala

These two are not mutually exclusive. If you want to perform GLM on the volume measures of each ROI, then the answer is yes. If you want to go a VBM style analysis, then no. On 12/9/2021 9:09 AM, Laura Willers de Souza wrote: External Email - Use Caution Hello FreeSurfer Developers,

Re: [Freesurfer] Interpreting Covariate Paired Analysis Results

Can you say more about your approach? Are you subtracting the two time points explicitly and computing a paired t? Or are you using the repeated measures anova approach. Send the FSGD file On 11/30/2021 11:04 AM, PDMD SRALab wrote: External Email - Use Caution We are using a paired a

Re: [Freesurfer] White matter

You can merge them yourself or you could run mri_annotation2label with one of the --lobes options to generate a new annotation of lobes, run use that to generate a new wmparc.mgz file (look in the recon-all.log file to get the command, specify your new annotation and change the output file name

Re: [Freesurfer] error in mri_sclimbic_seg

Hard to say what is going wrong from that. Can you try removing the trailing "/" from the subject name? Also, do you need --conform? Often the recon-all output is already conformed, so --conformed is not usually needed. It would be interesting to know if this is making it fail. On 12/6/2021 5:

Re: [Freesurfer] Definition of Premotor Area

Is the problem that there is an overlap? The exvivo labels and aparc labels are not going to be mutually exclusive. On 12/6/2021 5:34 PM, Tsolaki, Evangelia C. wrote: External Email - Use Caution Hello Freesurfer Team, I am interested in using premotor, precentral gyrus and postcentr

Re: [Freesurfer] question about surface registration to an average surface

How did you create the new MNI chimp average surface? On 12/5/2021 11:08 AM, Trisanna Sprung-Much wrote: External Email - Use Caution Hi Bruce So I have 77 chimp scans reconstructed in FS (NOT registered to MNI space, but rather a chimp volume template, to avoid scaling). After a lo

Re: [Freesurfer] Questions about GLM

If you run it with --eres-save, it will save the residuals in eres.mgh On 12/4/2021 11:17 AM, Laura Willers de Souza wrote: External Email - Use Caution Hello FreeSurfer Developers, I would like to assess whether my regression model meets the GLM assumptions, especially if there is n

Re: [Freesurfer] mri_label2label: one-to-one for subjectNo --> ico

Don, can you send your command line? If you are using surface-based registration, then the origin should not matter. You are right that there is not a one-to-one correspondence. The way it works  is that it starts on the target surface, goes through all the vertices and finds the closest vertex

Re: [Freesurfer] Help

defects are. On 11/29/2021 9:41 AM, Nilab Nasrullah wrote: External Email - Use Caution Sure. See attached. //Nilab *From:* Douglas N. Greve *Sent:* 29 November 2021 15:40 *To:* Nilab Nasrullah ; freesurfer

Re: [Freesurfer] mri_gcut gives "error: Could not set locale"

are you just running gcut or all of recon-all? If all of recon-all, please send the recon-all.log file On 12/2/2021 2:43 PM, Vishal Mohanty wrote: External Email - Use Caution Hi This is Vishal Mohanty, a Research Assistant at the CNS Lab

Re: [Freesurfer] Qdec error

We are not supporting qdec anymore. Try using the "command line stream", ie, mris_preproc, FSGD, etc On 12/1/2021 6:47 PM, Arian Klows wrote: External Email - Use Caution  Dear FS experts, I have freesurfer-linux-centos7_x86_64-7.1.1 on my computer and when I run qdec, I get the fol

Re: [Freesurfer] FSGD file

There is no way to model a missing cell in the FSGD. You'd have to figure out a value (eg, using imputation) or exclude those subjects On 11/30/2021 2:59 PM, Laura Willers de Souza wrote: External Email - Use Caution Hello FreeSurfer Developers, I would like to know what I put in the

Re: [Freesurfer] REtrieve perimeter from generated surfaces

sorry, I don't know what you mean by perimeter On 11/29/2021 8:09 PM, Fernanda Hansen P. de Moraes wrote: External Email - Use Caution Dear FreeSurfer experts, Is there a way to estimate the perimeter from a surface (e.g. ?h.pial) for each slice in an automated manner at any orientat

Re: [Freesurfer] Information on anova 2x2 longitudinal design

you need to run it as a DOSS, ie, --fsgd Repeted_measure.fsgd  doss On 11/29/2021 6:50 PM, std...@virgilio.it wrote: External Email - Use Caution Hi list, I have two groups undergoing two different treatments: one's placebo (n=12), one's drug (n=12). Two timepoints, at baseline (T1,

Re: [Freesurfer] Errors with mkanalysis-sess: missing file fmcpr.brainmask.fsaverage.lh

mask flag would be helpful? *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Monday, November 29, 2021 12:28 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Errors

Re: [Freesurfer] editing the aseg.mag using another tool and then rerunning

On 11/29/2021 11:55 AM, Alexopoulos, Dimitrios wrote: External Email - Use Caution A quick question. Is it feasible or even possible to edit the aseg.mgz  using another program (i.e. ITK-snap after converting to nifti), and rerunning the pipeline using the revised aseg as input T

Re: [Freesurfer] Errors with mkanalysis-sess: missing file fmcpr.brainmask.fsaverage.lh

In your mkanalysis command, why are you specifying the mask and the funcstem? These are tricky options to get right ... On 11/29/2021 9:50 AM, Hiersche, Kelly J. wrote: External Email - Use Caution Hello FreeSurfer Developers, First, I am new to using Freesurfer, so I apologize if an

Re: [Freesurfer] Smoothing and ROI averages from .stats output

Right. Actually, I don't think it would apply the smoothing to the annotation anyway On 11/29/2021 10:43 AM, Daniel Westfall wrote: External Email - Use Caution Good afternoon, It is my understanding that if I am only interested in the already averaged region ROIs that are output in

Re: [Freesurfer] Help

different format. Thanks, Nilab *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* 29 November 2021 04:01 *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Help Can you send some

Re: [Freesurfer] Visualization error in freeview from recon-all

sorry, no picture attached. Can you resend? On 11/29/2021 2:40 AM, achille.teil...@chu-lyon.fr wrote: External Email - Use Caution Dear experts, We are working with a large MRI dataset (FLAIR, T1) and we are performing recon-all based on the 3D T1. At the end, no error is detected b

Re: [Freesurfer] FREESURFER Recon all problem

If they are not part of the T1w series, then you can delete them (but then they should not have caused the error). If they are part of the series, then they are probably corrupted or perhaps the output of a very aggressive anonymization. On 11/25/2021 8:40 AM, Alison McDonnell wrote:    

Re: [Freesurfer] SynthSR

my best, AJ Scanners used for controls and test subjects: Achieva_TFE_R1 Achieva_TFE_R2 Ingenia_R1 Ingenia_R2 GE_SPGR_1529_R1 GE_SPGR_1529_R2 GE_SPGR_R1 GE_SPGR_R2 Phillip_Achieva_R1 Achieva_R2 GE_R1 GE_R2 On Sun, Nov 28, 2021, 20:41 Douglas N. Greve wrote: Also samseg, see *

Re: [Freesurfer] fsaverage_sym lobes parcellation mri_annotation2label

This is a bug. I've put a new version of mri_annotation2label here: https://gate.nmr.mgh.harvard.edu/safelinks/greve/ username 'guest' password 'collab' copy it into $FREESUFER/bin (after making a copy of the one that is there). On 11/22/2021 12:23 PM, Dr. Cornelius Kronlage wrote: > Ex

Re: [Freesurfer] Surface-based smoothing of EPI data

That will work; it may be clearer to use mris_fwhm, eg, mris_fwhm --smooth-only --s sub-0006 --hemi lh --fwhm 5 --cortex --i input --o output On 11/26/2021 6:48 AM, Mason Wells wrote: External Email - Use Caution Hi Experts, This question may have been addressed elsewhereon the lis

Re: [Freesurfer] Can't load ROI labels

For volumes, load labels using the "Load ROI..." under the File menu For surfaces, use the "Load" button in the "Label" section On 11/23/2021 2:44 PM, Shapiro, Noah Lorenz wrote: Hello, I am very new to FreeSurfer, and I was going through the tutorials and bumped into difficulties when loading

Re: [Freesurfer] FREESURFER Recon all not working

Just add -cw256 to the recon-all command line On 11/23/2021 8:34 AM, Alison McDonnell wrote: External Email - Use Caution Hi Tim, I looked at orig.mgz and it seemed fine and could see the whole head. i dont know what is meant by the flag -cw256 error. I am taking over a project from

Re: [Freesurfer] Help

Can you send some pictures? On 11/23/2021 4:02 AM, Nilab Nasrullah wrote: External Email - Use Caution Hi, I am editing subjects for a research project. After reconstruction, some parts of the brain are not included in the segmentation. Often, some parts of the temporal lobe and the

Re: [Freesurfer] register.dat

Yes, but if there is an anat2orig2diff.bbr.lta file, use that instead On 11/22/2021 12:48 PM, Zeng, Qi wrote: External Email - Use Caution Sorry for the trouble, I seemed to find the registration matrix located in xfms/anatorig2diff.bbr.dat. Is that one correct? Best, Jackie On M

Re: [Freesurfer] Difficulty Running Single Subject Surfaced Based GLM

I noticed that you are explicitly setting the mask and funcstem in mkanalysis-sess. Is there a reason for that? Also, I'd set -poly to 5. On 11/21/2021 1:11 PM, Hiersche, Kelly J. wrote: External Email - Use Caution Hello FreeSurfer Developers, First, I am new to using Freesurfer, so

Re: [Freesurfer] interhemispheric registration: xhemi vs. mris_left_right_register

I see what you mean, though I don't think either one look that great. The first thing to do is to backup and look at the registration to fsaverage_sym by mapping the lh and rh curv to lh.fsaverage_sym and see if the curv patterns match up with those in fsaverage_sym and to each other (use mris_

Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Help: Using a Different Atlas for Anatomical ROI Analysis

That is a label atlas; you cannot run that through FS. You will need a t1-weighted image to use as input to recon-all to start. On 11/19/2021 1:59 PM, Flanagan, Shawn D wrote: External Email - Use Caution Hello, I would like to use the Brainnectome atlas for cortical thickness analy

Re: [Freesurfer] SynthSR

Also samseg, see https://pubmed.ncbi.nlm.nih.gov/33940143/ On 11/26/2021 11:16 AM, Fischl, Bruce wrote: Hi AJ you might try SynthSeg, as that is one of the advantages of it - it isn't biased towards any particular MRI sequence cheers Bruce

Re: [Freesurfer] Freesurfer v7.x and bias correction -3T option not working

Hi Christine, yes, your interpretation is correct. The -3T flag only applied when using the mni tools, so it has no effect with ANTS. What was the nature of the failure? We might be able to tweak the ANTS command line to improve it. doug On 11/15/2021 12:52 PM, Notestine, Christine wrote:  

Re: [Freesurfer] recon-all error with T1 dcm images

it is not clear why it failed. Can you look at  nu.mgz to see if anything looks weird about it? On 11/18/2021 1:43 AM, Wei Shao wrote: External Email - Use Caution Hi, Dear Freesurfer experts I'm have met a recon-all errors with data collected recently like this ADNI_002_S_6652_MR_Ac

Re: [Freesurfer] "Vertex Talairach" in tksurfer?...

They are mni305 coordinates On 11/19/2021 9:41 AM, Gonzalo Rojas Costa wrote: > External Email - Use Caution > > Hi: > > "Vertex Talairach" in tksurfer: how does it relate to MNI coordinates? > > Sincerely, > > > Gonzalo Rojas Costa > Department of Radiology > Clínica las Condes >

Re: [Freesurfer] MNI coordinates to vertex...

have you looked at this page? https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 11/19/2021 9:15 AM, Gonzalo Rojas Costa wrote: > External Email - Use Caution > > Hi: > >I have MNI 152 coordinates equivalent to 10-10 and 10-20 EEG > electrodes (see Supplementary Tables 1 a

Re: [Freesurfer] V5 / v7

don't know. try figuring out which step is actually changing On 11/18/2021 2:03 PM, Brusaferri, Ludovica wrote: Hi! I am using a pipeline that was implemented and validated using fs 5.3 , which does the following: * compute transformation matrix for linear registration of SUV with T1-2mm, wi

[Freesurfer] Fwd: OpenNeuroPET hackathon at MGH -- Dec 6th and 7th

For those interested in PET and BIDS, this should be pretty useful. Forwarded Message Subject:OpenNeuroPET hackathon at MGH -- Dec 6th and 7th Date: Wed, 17 Nov 2021 19:31:48 -0500 From: Wighton, Paul To: Greve, Douglas N.,Ph.D. Hi Doug, I was hoping you c

Re: [Freesurfer] Using Mri_vol2surf

R: Option T2.reg is unknown" *Gesendet:* Mittwoch, 17. November 2021 um 16:11 Uhr *Von:* "Douglas N. Greve" *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] Using Mri_vol2surf Can you be more specific about why it is not working? You definitely need to run bbregister t

Re: [Freesurfer] [recon-all error] Excessive topologic defect encountered

wow, that is weird. The RH extends far into the LH. What does the aseg.presurf.mgz look like? Are the cortices and WM properly separated left-right? On 11/15/2021 4:33 AM, Alec Süwolto wrote: External Email - Use Caution Hello freesurfers, I’m new to freesurfer and I can’t fix a har

Re: [Freesurfer] FREESURFER - Re-con all problems

You need to tell it what to do, eg, -all to do everything. On 11/15/2021 8:49 AM, Alison McDonnell wrote: External Email - Use Caution recon-all.log is attached. have tried to run again with different data and had the same problem On Wed, 10 Nov 2021 at 22:39, Douglas N. Greve

Re: [Freesurfer] FSGD and Contrast file for scanner and sex correction

You have 16 groups so you need 16 items in the contrast vector (assuming no continuous variables), so you need something like -1 +1 repeated 8 times to give you 16 On 11/17/2021 7:23 AM, Thalhammer, Melissa wrote: External Email - Use Caution Dear Freesurfers, I am struggling with t

Re: [Freesurfer] Using Mri_vol2surf

Can you be more specific about why it is not working? You definitely need to run bbregister to create a registration file On 11/17/2021 7:09 AM, m-maiw...@web.de wrote: External Email - Use Caution Dear List, I first run the recon-all stream using a MPRAGE as input, then bbregister t

Re: [Freesurfer] recon-all

Does that file exist? Have you manually/visually checked that subject? Probably recon-all just did not finish On 11/17/2021 12:13 AM, a Chinese reader wrote: External Email - Use Caution Dear Freesurfer experts, When I run the command "recon-all -s <> -qcache" , ERROR: cannot find /h

Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

I'm not sure what is happening. Does it work without the parallel flag? btw, you are not using 7.2 here's your build: build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-dev-20210824-e101185 On 11/16/2021 4:26 PM, Peled, Noam wrote: Dear Freesurfer group, I was running recon-all (Freesurfer 7

Re: [Freesurfer] Freesurfer: Re-run recon-all in older versions

FS 6. Best, El vie., 12 nov. 2021 15:51, Douglas N. Greve escribió: If you are going from 5.3 to 6, you should just be able to run recon-all -all on the 5.3 folder and it should take into account your previous edits (make a copy first though:) On 11/12/2021 4:40 AM, Steve

Re: [Freesurfer] Transform matrix

Have you seen this page? https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 11/12/2021 6:23 AM, Alberto Del Cerro Leon wrote: External Email - Use Caution Hello Freesurfer team, I did a white matter atlas from surface annot with mri_aparc2aseg. However, when I use this

Re: [Freesurfer] Freesurfer: Re-run recon-all in older versions

If you are going from 5.3 to 6, you should just be able to run recon-all -all on the 5.3 folder and it should take into account your previous edits (make a copy first though:) On 11/12/2021 4:40 AM, Steve Petersen wrote: External Email - Use Caution Dear all, We conducted the recon-

Re: [Freesurfer] FsFastFunctionalConnectivityWalkthrough

On 11/12/2021 3:29 AM, Alice Giubergia wrote: External Email - Use Caution Thanks for your replies Doug! I copied the previous messages below, since I did not menage to retrieve the original email. 1) Thanks. 2) Regarding question number 2, yes that was what I meant. 3) I ran the t

Re: [Freesurfer] permutation simulation errror

*From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursday, November 11, 2021 5:39 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] permutation simulation errror What do you get if you run stem2fname /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitle

Re: [Freesurfer] permutation simulation errror

Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779 *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursday, November 11, 2021 3:46 PM *To:* freesurfer

Re: [Freesurfer] permutation simulation errror

Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779 *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursday, November 11, 2021 3:05 PM *To:* freesurfer

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

Qi On Thu, Nov 11, 2021 at 3:28 PM Douglas N. Greve wrote: For the DOSS case, yes. On 11/11/2021 3:23 PM, Zeng, Qi wrote: External Email - Use Caution Hi  Douglas, If to set up the FSGD as below, is my design matrix for case and control comparison as "1

Re: [Freesurfer] permutation simulation errror

behalf of Douglas N. Greve *Sent:* Thursday, November 11, 2021 2:27 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] permutation simulation errror That is for mri_glmfit, not mri_glmfit-sim. On 11/11/2021 3:24 PM, Brown, Alexander wrote: External Email - Use Caution

Re: [Freesurfer] permutation simulation errror

Francke Drive Columbia, MO 65211 Contact: 573-884-8779 *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursday, November 11, 2021 2:04 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

ite   81.3   1558515.86 Best, Qi On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve wrote: I would advice setting up the FSGD files with 8 classes based on your 3 discrete, 2-level variables, eg, MaleControlWhite then use two continuous variables Age and eTIV. You should definitely

Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats

en nombre de Douglas N. Greve *Enviado:* miércoles, 10 de noviembre de 2021 15:09 *Para:* freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats Ah, I see. Can you upload those two subjects using the method below? From the linux command line, Creat

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

uot;White"1187649.47 or 3) Variables AgeGenderRaceeTIV InputSub001_base"Control"85"Female""White"1350519.71 InputSub002_base"Control"81.3 "Male""White"1558515.86 InputSub003_base"Control"72.7 "Male""White"

Re: [Freesurfer] permutation simulation errror

...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Wednesday, November 10, 2021 4:40 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] permutation simulation errror WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in

Re: [Freesurfer] [Re]:FsFastFunctionalConnectivityWalkthrough

sorry, can you include the previous emails in this thread along with your new questions? On 11/11/2021 11:44 AM, Alice Giubergia wrote: External Email - Use Caution Thanks for your replies Doug! 1) Thanks. 2) Regarding question number 2, yes that was what I meant. 3) I ran the task a

Re: [Freesurfer] "No such file or directory" in wm

You cannot use flair as the main input. It has to be t1w; you can only use flair as an additional input to help fix the pial surface On 11/11/2021 2:30 PM, Devarajan, Alex wrote: External Email - Use Caution Hello, I'm running a fairly large database of MRIs through freesurfer for a

Re: [Freesurfer] turning a surface label into 3d object

You can create a "patch" with something like label2patch -surf white  fsaverage lh  lh.V1_exvivo.label ./lh.patch then load it with tksurferfv fsaverage lh white -patch ./lh.patch When you load a patch, you will only be able to see the patch of the surface that you loaded it on If you want to be

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

rror: Input line 1, subjid = sub001_base  Variable 2 has character string Female  Variables should be continuous numbers FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input Also attached FSGD file below. Thank you so much for the help! Best, Zeng On Wed, Nov 10, 2021 at 5:41 PM Douglas N. G

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

please send your command line and full terminal output as well as the fsgd file On 11/10/2021 5:12 PM, Zeng, Qi wrote: External Email - Use Caution Hi Freesurfer experts, Here, I want to design a simple group comparison (two levels: Case vs. Control) and also count for 4 covariates 

Re: [Freesurfer] permutation simulation errror

Which version of FS are you using? Can you send the log file created by mri_glmfit-sim (different than the one you sent)? On 11/10/2021 3:49 PM, Brown, Alexander wrote: External Email - Use Caution Hello, I am attempting to run a permutation simulation to correct for multiple compar

Re: [Freesurfer] FREESURFER - Re-con all problems

And send the recon-all.log file On 11/10/2021 10:57 AM, Alison McDonnell wrote: External Email - Use Caution the full line after setting up the environment is recon-all -i /Users/ali?Arch_Raim/IM-0001-0001.dcm -s IM-0001 -all On Wed, 10 Nov 2021 at 15:53, Tim Schäfer

Re: [Freesurfer] FsFastFunctionalConnectivityWalkthrough

On 11/10/2021 9:48 AM, Alice Giubergia wrote: External Email - Use Caution Dear FreeSurfer experts, I'm interested in performing a functional analysis on task-based data. I was taking as an example the "FsFastFunctionalConnectivityWalkthrough" tutorial but, if I got it correctly,

Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats

e spam. Many thanks, Gonzalo. *De:* freesurfer-boun...@nmr.mgh.harvard.edu en nombre de Douglas N. Greve *Enviado:* martes, 9 de noviembre de 2021 20:13 *Para:* freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 ap

Re: [Freesurfer] Aseg and wm edits? + white/pial overlap near subcortical structures

It will be safest if you use the same command (in the sense that all the files will be up-to-date). If the surfaces are ok and you really don't want to regenerate them, then I think you can just use recon-all -s subject -aparc2aseg -segstats There may be some operations that will see that the ase

Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats

? *De:* freesurfer-boun...@nmr.mgh.harvard.edu en nombre de Douglas N. Greve *Enviado:* martes, 9 de noviembre de 2021 18:09 *Para:* freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2

Re: [Freesurfer] temporal filtering and nuisance regression

They are done simultaneously On 11/9/2021 11:38 AM, Turnbull, Adam wrote: External Email - Use Caution Hello, I just wanted to confirm whether Freesurfer performs temporal filtering simultaneously with nuisance regression, or whether it performs these steps subsequently in either

Re: [Freesurfer] smoothing images using mri_surf2surf command line

ply a gifti image with 10242 vertices and 475 time points. The following is the information: Screenshot 2021-11-09 at 16.47.58.png Do I need to transfer the images to you? On Tue, 9 Nov 2021 at 16:26, Douglas N. Greve wrote: I have a feeling that it may be ignoring the extra frames i

Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats

-boun...@nmr.mgh.harvard.edu en nombre de Douglas N. Greve *Enviado:* martes, 9 de noviembre de 2021 14:49 *Para:* freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats ⚠ Caution: External sender The white surface won't change, but the pial su

Re: [Freesurfer] smoothing images using mri_surf2surf command line

smoothing output with n = 2 Saving target data Saving to /Volumes/NatureNurtu/NatureNurture/Neuroimaging/RSFC/Preprocessing/fmriprepRFS/sub-eb01/sub-eb01_task-resting_space-fsaverage5_hemi-L_desc-regressedFilteredSmoothed.func.gii Best, Yangwen On Tue, 9 Nov 2021 at 15:49, Douglas N. Greve wrote

Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats

The white surface won't change, but the pial surface should change. Can you verify that the pial surface changed? On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote: External Email - Use Caution Hello, I wanted to compare the results of the aparc.stats on the same subjects when only t

Re: [Freesurfer] smoothing images using mri_surf2surf command line

please send your command line and terminal output On 11/9/2021 6:05 AM, Yangwen Xu wrote: External Email - Use Caution Hello FreeSurfer Developers, I am trying to smooth images using mri_surf2surf. Here is the command line: 'mri_surf2surf --s fsaverage5 --hemi lh --cortex --sval ',I

Re: [Freesurfer] Brain Volume Extraction

You could run it up to the skull stripping (-autorecon1), then compute the brain volume yourself from the skull-stripped image. You could also use samseg; samseg only takes an hour or so to run and outputs a measure of total intracranial volume, but you could also extract total brain volume fro

Re: [Freesurfer] Aseg and wm edits? + white/pial overlap near subcortical structures

On 10/29/2021 10:46 AM, Kang, Jee Won wrote: External Email - Use Caution Hello all, There are two topics I would appreciate your expert advice on: Topic 1: Aseg and wm edits I was going through the wiki and the archive of past inquiries and was unable to find a clear answer to

Re: [Freesurfer] Confusion about discrete variable in the FSGD file

On 10/27/2021 11:39 AM, Douglas N. Greve wrote: Dealing with discrete variables as discrete is the way I would do it as you would not have any reason to think that there is some linear relationship between your the (arbitrary) values you assign to discrete variables and thickness. Age is

Re: [Freesurfer] adding covariates to a longitudinal glmfit model

On 10/29/2021 10:39 PM, Zeng, Qi wrote: External Email - Use Caution Hi Experts, After completing long_mris_slopes to get the rate of change and then concatenating them into one.mgh file for group analysis (mris_preproc). I am finally getting to mris_glmfit. Got a couple of questi

Re: [Freesurfer] tksurfer

You can use tksurferfv (this is a frontend for freeview that takes most of the original tksurfer options) On 11/3/2021 1:11 PM, Fischl, Bruce wrote: Hi Arian Tksurfer has been deprecated for a long time. Can you try freeview instead? Bruce *From:* freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] mri_label2label issues

/ /McGill University / /Montreal Neurological Institute/ *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Wednesday, November 3, 2021 11:08 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject

Re: [Freesurfer] surface labels to volume masks in MNI space

So you want to map the labels in fsaverage into MNI152 volumes pace, right? After mris_divide_parcellation, you should have a parcellation in fsaverage space. Use mri_surf2surf (or mris_apply_reg) to map that into the MNI152 that you ran recon-all on. Look in the recon-all.log file for the comm

Re: [Freesurfer] mri_label2label issues

Did you see this response from a few days ago? On 10/27/2021 11:26 AM, Douglas N. Greve wrote: I'm not sure what you did or how to interpret that pic. If I understand, you ran a case through recon-all and created labels on that case. You then recon-all again using a totally different o

Re: [Freesurfer] PETsurfer

There is nothing special you have to do. What version of FS do you have? You still have to source the FS environment. If you can run recon-all, you should be able to run PETsurfer On 11/1/2021 12:26 PM, Brusaferri, Ludovica wrote: Hi! I have been using freesurfer regularly and I am now trying

Re: [Freesurfer] Registering DTI fiber tracts (from MRtrix3) to FreeSurfer registered surfaces.

To add on to that, dt_recon will register you DTI to the FreeSurfer anatomical analysis. It will on generate FA, diffusivity, etc. I don't know how to get that interfaced with output from MRtrix3 On 10/29/2021 5:09 PM, Mora, Jocelyn S. wrote: Hi Reshma, Yes, you would use the FreeSurfer Longi

Re: [Freesurfer] Total volumes SAMSEG

That is what I would do. The FS WM volumes are computed using the surface, so it will be more accurate (and probably a little bigger) On 10/29/2021 3:59 AM, Nederpelt, D.R. van (David) wrote: External Email - Use Caution External Email - Use Caution Dear SAMSEG developers, I

Re: [Freesurfer] Magnetization Transfer Images and recon-all

You did not send your recon-all command but my guess is that it stopped without error because you did not include a directive (eg, -all). But in any event, you cannot run an MT image through recon-all On 10/29/2021 3:35 AM, Marlene Tahedl wrote: > External Email - Use Caution > > Hi! >

Re: [Freesurfer] orig/001.mgz to brain.mgz transformation?

There are answers embedded in your email On 10/27/2021 12:36 PM, Billah, Tashrif wrote: Thank you Douglas, I enjoyed reading your referral. However, I did not get answer to any of my questions. Can you take a second look? Best, Tashrif Date: Wed, 27 Oct 2021 11:41:35 -0400 From: "Doug

Re: [Freesurfer] manual segmentation

not sure what you mean by "manual segmentation" or why you would do that again. We do recommend at least inspecting the data visually On 10/27/2021 11:35 AM, 刘卫 wrote: External Email - Use Caution Hello FreeSurfer Developers, I would like to ask, on free surfer, can I directly analyz

Re: [Freesurfer] orig/001.mgz to brain.mgz transformation?

On 10/27/2021 10:58 AM, Billah, Tashrif wrote: Hi, 1. What is the name of the space of wmparc.mgz? I see that it is in the same space of brain.mgz. Yes 1. 2. What transform file brings orig/001.mgz to brain.mgz? See https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

Re: [Freesurfer] Confusion about discrete variable in the FSGD file

Dealing with discrete variables as discrete is the way I would do it as you would not have any reason to think that there is some linear relationship between your the (arbitrary) values you assign to discrete variables and thickness. Age is not an arbitrary value, so I would use that as a con

Re: [Freesurfer] recon-all missing files

We have not used COR format in years. Why do you need it? On 10/26/2021 3:17 PM, Alireza Karami wrote: External Email - Use Caution Hello I used the following command to create the surface of my subject: recon-all -s subj -i anat.nii -all -qcache -3T However, some files are missing f

Re: [Freesurfer] A question regarding a Freeview command

I don't think there is anything specific for the --table option, but everything else is the same. On 10/24/2021 4:31 PM, Alvarado,Luis R wrote: External Email - Use Caution Hi Douglas, I was wondering if there are any “--table option” specific tutorial for the mri_glmfit function. I

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