[Freesurfer] mri_histo_atlas_segmen/ mri_synthseg errors (on MacBook M1 pro)

ns! I know that running the analysis on a MacBook might not be the best choice anyways, but before I try to set it up on our institute HTC (which might be a whole other challenge), I though I try it that way. Also, I figured someone might be interested in the error report. Thanks a lot! B

[Freesurfer] Common space

External Email - Use Caution Good morning, I would be interested in observing regional differences in cortical thickness without using predefined regions. However the results offered by FreeSurfer arrange the thickness results etc. in an individual space which is difficult to compa

[Freesurfer] Aparc2aseg citation

External Email - Use Caution Hi FS team, for my line of research I have used aparc2aseg with the --labelwm --hypo-as-wm option to obtain wm measurements from a custom atlas of the brain lobes. However I don't know how I should cite this method as the aparc2aseg documentation does n

[Freesurfer] WMH in aparc+aseg

External Email - Use Caution Hello FS team! I am using the volumetric data of WMH obtained during the recon-all in the apar+aseg.mgz file. Where I could find the description of the method throught it is segmented? I find the Automated Labeling of Neuroanatomical Structures in the

Re: [Freesurfer] SAMSEG

, > > Koen > > > On Fri, Aug 12, 2022 at 10:51 AM Alberto Del Cerro Leon < > bertocer...@gmail.com> wrote: > >> External Email - Use Caution >> >> Hello, I am reading the paper "A contrast-adaptive method for >> simultaneous whole-brain

[Freesurfer] SAMSEG

External Email - Use Caution Hello, I am reading the paper "A contrast-adaptive method for simultaneous whole-brain and lesion segmentation in multiple sclerosis" relative to SAMSEG method and I would like to ask you a question. Due to the use of a training set in the lesion shape

[Freesurfer] Problem with labels

External Email - Use Caution Hello Freesurfer Team, I am trying to use a ROI to create a label into fsaverage. Once I registered my ROI to the fsaverage space I performed a mri_vol2surf and mri_cor2label to obtain a label of the ROI on the fsaverage surface. However, this label has

[Freesurfer] Transform matrix

External Email - Use Caution Hello Freesurfer team, I did a white matter atlas from surface annot with mri_aparc2aseg. However, when I use this atlas in comparison with the original T1 I have observed that both images don't share the transformation matrix. Do you know how I could I

[Freesurfer] SAMSEG thresholds

External Email - Use Caution Hello FreeSurfer team, I have a question about SAMSEG thresholds. I am analyzing the vascular lessions aplying several thresholds. I would expect that lower thresholds results in lower volumes but dont seems like that. What is the reason? __

Re: [Freesurfer] Error in SAMSEG preprocessing

; > Andrew > > > > *From: *freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alberto Del Cerro > Leon > *Date: *Friday, May 7, 2021 at 6:49 AM > *To: *Freesurfer support list > *Subject: *[Freesurfer] Error in SA

[Freesurfer] Error in SAMSEG preprocessing

External Email - Use Caution Hello, I am trying to use SAMSEG to segment white matter lesions, I ran the following command: run_samseg --input '/home/neuroimage/fsl/vascular/1002/U1002_3DT1.nii' '/home/neuroimage/fsl/vascular/1002/flair_reg.nii' --pallidum-separate --lesion --lesi

[Freesurfer] help with SAMSEG

External Email - Use Caution Hello Freesurfer team, my group is interested in using the SAMSEG tool to evaluate white matter lesions in MCI patients. We would like to use a personalized atlas for the measure. We suppose that we need to use the flag --atlas but we don`t know if we n

Re: [Freesurfer] Problem with freesurfer measures

ity-name norm --in-intensity-units MR --subject 218 --surf-wm-vol --etiv* El lun, 5 abr 2021 a las 15:50, Douglas N. Greve () escribió: > What are your command lines? > > On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote: > > External Email - Use Caution > Thanks a lot, It works

Re: [Freesurfer] Problem with freesurfer measures

e 3000s and > 4000s in $FREESURFER_HOME/FreeSurferColorLUT.txt > > > On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote: > > External Email - Use Caution > Hello Douglas, i tried but when i look at the wmparc.mgz created by the > code >>mri_aparc2aseg --s

Re: [Freesurfer] Problem with freesurfer measures

ng the aparc annot to your annot and the output to a new > file name. Look in wmparc.stats; at the top will be an mri_segstats command > line. Copy that command line changing the file names as needed. > > On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote: > > External Email -

Re: [Freesurfer] Problem with freesurfer measures

> On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote: > > External Email - Use Caution > I want to use the annotation file created by myself in fsaverage to > calculate the anatomical stats, but i dont know what is the best workflow. > > 1. Convert the annotation fi

Re: [Freesurfer] Problem with freesurfer measures

> > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del Cerro > Leon > *Sent:* Monday, March 8, 2021 7:02 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Problem with freesurfer measures >

[Freesurfer] Problem with freesurfer measures

External Email - Use Caution Hello Freesurfer team, I am using an annotation file that i've created previously to obtain the measures of some ROIs. To do that i am using de commands mri_surf2surf and mri_segstats. I want to obtain the following measures: 1. Gray and White Matter Vo

Re: [Freesurfer] Hippocampal segmentation

Del Cerro Leon wrote: > > External Email - Use Caution > Hello Freesurfers, I am doing an AAL atlas on freesurfer using > mri_vol2surf and editing the labels manually. However when I was editing > the labels in tksurfer the hippocampal field is quite bad. I tried to look > t

[Freesurfer] Hippocampal segmentation

External Email - Use Caution Hello Freesurfers, I am doing an AAL atlas on freesurfer using mri_vol2surf and editing the labels manually. However when I was editing the labels in tksurfer the hippocampal field is quite bad. I tried to look the segmentation used by you in labels but

[Freesurfer] vascular damage meassures

External Email - Use Caution Hello Freesurfer, my lab is interested in measuring the vascular damage in different subjects. I read that Freesurfer can measure the hypointesities characteristic of brain damage in an automated way. However I couldn't find the properly workflow to do

Re: [Freesurfer] help with labels

hat it intersects the segmentation at all > vertices. You can find the vertex numbers for the holes, and then go > specifically to that vertex > > On 1/27/2021 6:27 AM, Alberto Del Cerro Leon wrote: > > External Email - Use Caution > Hello Freesurfer team, I did an AAL

[Freesurfer] help with labels

External Email - Use Caution Hello Freesurfer team, I did an AAL atlas on the surface using mri_vol2surf, however when I look at this overlay there are many holes in the labels with vertices that don't belong to any label. Could u help me with this problem?

[Freesurfer] Holes in my ROIs

External Email - Use Caution Hello Freesurfers, I created surface image based on AAL with mri_vol2surf. However i see that in some regions there are a lot of holes, i thought that probably is for the presence of subcortical regions in the AAL.ni. There is some workflow to select th

Re: [Freesurfer] asegstats2table {Disarmed}

(661) 904-3534 > > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alberto Del Cerro > Leon > *Sent:* Friday, December 11, 2020 6:57 AM > *To:* Freesurfer support list > *Subject:*

Re: [Freesurfer] labels in the surface {Disarmed}

2020 a las 18:50, Greve, Douglas N.,Ph.D. (< dgr...@mgh.harvard.edu>) escribió: > This might be the way it is given that the AAL is volume-based and you are > trying to put it on the surface. What is your vol2surf command? > > On 12/10/2020 6:59 AM, Alberto De

[Freesurfer] asegstats2table

External Email - Use Caution Hello Freesurfers, I have a question about the command asegstats2table. I want to obtain the structural data of a group set based on labels created by myself. I see that this is possible with mris_anatomicalstats for 1 subject but can I obtain the data

Re: [Freesurfer] About mri_vol2surf {Disarmed}

> On 11/30/2020 8:31 AM, Alberto Del Cerro Leon wrote: > > External Email - Use Caution > First of all, thanks you Douglas for the support. > As I said i run the mri_vol2surf and I obtained an error: > > mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheade

Re: [Freesurfer] About mri_vol2surf {Disarmed}

t; Can you send the full terminal output? > > On 11/18/2020 6:41 AM, Alberto Del Cerro Leon wrote: > > External Email - Use Caution > I tried to run mri_vol2surf with the following command: mri_vol2surf --src > /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI -

[Freesurfer] mri_vol2surf

External Email - Use Caution Hello, I am trying to run mri_vol2sur to obtain the AAL atlas on freesurfer. i used this command line "mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img"

[Freesurfer] mri_vol2surf

External Email - Use Caution Hello, I have a couple of questions: 1. I asked before how to obtain AAL labels on Freesurfer. I am following your instructions, but I don't know how to load the AAL onto my T1w template to ensure everything aligns 2. Secondly, I tried to run mri_vol2

Re: [Freesurfer] About mri_vol2surf {Disarmed}

ut before you do that , load the AAL atlas onto the > mni152subject with the surfaces to make sure everything aligns. You might > want to do this with the colin27 brain instead because I think that is what > the AAL atlas is defined on. > > On 11/16/2020 5:30 AM, Albe

Re: [Freesurfer] About mri_vol2surf {Disarmed}

> > On 11/16/2020 5:30 AM, Alberto Del Cerro Leon wrote: > > External Email - Use Caution > Hello everyone, I tried to follow your instruction about how to get the > fresurfer stats in AAL ROIs. I have an image .nii with the labels of the > AAL in the MNI space (i subm

[Freesurfer] About mri_vol2surf

External Email - Use Caution Hello everyone, I tried to follow your instruction about how to get the fresurfer stats in AAL ROIs. I have an image .nii with the labels of the AAL in the MNI space (i submit this image in the e-mail). Can I use this image in the mri_vol2surf? If so, i

Re: [Freesurfer] Help with MRI labels {Disarmed}

t; AAL anatomical T1w volume template, then use mri_vol2surf to sample the > labels on the surface, then use this surface segmentation or extract labels > (mri_cor2label with --surf option) or convert to an annotation > (mris_seg2annot) > > > On 11/11/2020 11:32 AM, Albe

[Freesurfer] Help with MRI labels

External Email - Use Caution Good afternoon, my name is Alberto del Cerro and I am a PhD student in the cognitive and computational neuroscience laboratory (LNCyC) at the biomedical technology center (CTB) of the Polytechnic University of Madrid (UPM). I am currently extracting the

[Freesurfer] cortical thickness f-test correction

--2spaces Thank you very much in advance! Sincerely, Leon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it

[Freesurfer] recon-all for non-human primates failed and what to do next?

. Could someone tell me what other strategies I could use to make it work? Many thanks in advance! Leon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail

Re: [Freesurfer] the make_average_subject without aparc.annot

Hi, Bruce Thanks for the information. I can wait for his information after he comes back. Best Leon From: Bruce Fischl To: Leon Cc: "freesurfer@nmr.mgh.harvard.edu" ; Douglas N Greve Sent: Wednesday, July 11, 2012 4:23 PM Subject: Re: [Frees

[Freesurfer] the make_average_subject without aparc.annot

and I was asked to input these annotation files that do not exist for non-human primate data. Many thanks! Leon Re: [Freesurfer] how to generate aparc.annotion files? Douglas N Greve Mon, 08 Nov 2010 09:55:49 -0800 It is needed in make_average_surface. I've created a new version that

[Freesurfer] no-aseg for make_average_subject

a surface without aparc.annot files? Thank you very much in advance! Leon  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the pers

[Freesurfer] how to save edited lh.white using matlab

tell how I can save edited ?h.white and pial surfaces using matlab functions? Many thanks Leon  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is

[Freesurfer] map ROI-based measures back to surface

the intensity differences between these 200 ROIs on surfaces. Could someone tell me what is the best way to realize that? Forgive me if this question has bee asked before, but I really do not know how to input best keywords for the question to search in the archive. Many thanks in advance! Leon

Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

f the ROI is identical as the one in the picture I attached in the previous email. Do you think it might be because the mri_label2vol overlooks the index of 0, as the intensity value in the volumes starts with 1? I would appreciate your help on this. Leon

[Freesurfer] exclude ROIs in an annotation file under a label

Hi, FreeSurfer experts I have one annotation file with many ROIs and one label file that denotes medial wall. Now I want to remove the ROIs in the annotation file that is covered by the medial wall. Is there any way that I can realize that in the surface space? Thank you! Leon

Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

Hi, Douglas I have uploaded the file to the system. Also, my new results showed that  when  ic3.tri (instead of ic2.tri) is used as the input, one ROI at the similar location is also missing. Hope it will help you diagnose.  Thanks Leon From: Douglas N

Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

a link in FS archive. The ID for the one you sent to me is: $Id: mri_label2vol.c,v 1.34.2.4 2011/09/30 15:19:36 greve Exp $ They look almost identical. Do you have any ideas what else may cause this issue and possible workaround? Thank you Leon From

Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

Fischl To: Leon Cc: FreeSurfer Sent: Friday, June 1, 2012 8:02 PM Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri Can you send us your command lines and screen output? On Jun 1, 2012, at 7:44 PM, Leon wrote: Hi, folks > > >when I transf

Re: [Freesurfer] transfer annot files from template to each subject

Hi, Bruce Thank you very much for your information and the codes. Best Leon From: Bruce Fischl To: Leon Sent: Friday, June 1, 2012 10:48 AM Subject: Re: [Freesurfer] transfer annot files from template to each subject p.s. here's a gzipped versi

Re: [Freesurfer] transfer annot files from template to each subject

ot be used to transfer ROIs between subjects, what is the difference between providing ?h.sphere and ?h.sphere.reg as the input surface? Thanks again for your help! Leon From: Bruce Fischl To: Leon Cc: FreeSurfer Sent: Thursday, May 31, 2012 2:37 PM S

Re: [Freesurfer] transfer annot files from template to each subject

am new to FreeSurfer and your help is greatly appreciated! Leon Re: [Freesurfer] mris_make_face_parcellation Franz Liem Mon, 13 Feb 2012 05:35:10 -0800 Dear Bruce, thank you so much for your reply; it seems to work now. However, a weird thing, I also mentioned in my previous post, still happ

[Freesurfer] transfer annot files from template to each subject

to do that? Many thanks in advance Leon  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. I

Re: [Freesurfer] Fw: wm surface does not follow wm.mgz

that corresponds to a surface-based template can be helpful if in the future I need to do both volume- and surface- based analyses and need to transfer ROIs between them. Correct me if my ideas are problematic since I am new to surface-based analyses. Many thanks

Re: [Freesurfer] Fw: wm surface does not follow wm.mgz

help! Leon From: Sebastian Moeller To: Leon Cc: FreeSurfer Sent: Friday, May 25, 2012 1:28 PM Subject: Re: [Freesurfer] Fw: wm surface does not follow wm.mgz Hi Leon, if I recall correctly the wm surface is looking at intensity gradients in the