[Freesurfer] aseg.stats file

Hi all, I need data which are in the aseg.stats file (which is in the stats file). Some patients haven't the aseg.stats file in the stats file, so does somebody know where I can find the aseg.stats file? Thanks Irene Mattisi Multiple Sclerosis Centre of Padova,

[Freesurfer] Skull strip

sal volume). Thank you, Irene ___ 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. If you believe t

[Freesurfer] Hippocampal subfield segmentation paused

Hi, there, I am running the hippocampal subfield segmentation on a high resolution T2 data that only covers the bilateral hippocampus and nearby temporal lobe areas.  Following the instruction on this webpage: http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation I used the com

Re: [Freesurfer] Hippocampal subfield segmentation paused

Hi, Eugenio, I have already sent the log files to you. And would you please give me a hint what is the right command for computing subfields with high-res T2? Thank you very much!! -Irene From: Juan Eugenio Iglesias To: Irene Lee Cc: "frees

Re: [Freesurfer] manual editing: skull strip

HI, I send you the table in attach, so you can see volumes differences. s47c is the subject edited also OUT of the pial surface. thank you, Irene 2014/1/10 Bruce Fischl > Hi Irene > > what changed and by how much? The ICV will change a bit, and because of > partial volume estimati

[Freesurfer] Post-doctoral position in brain development in NeuroSpin, Paris

The team of “brain development imaging” (Gif-sur-Yvette, France) offers a 2-year post-doctoral position from September 2013, on the study of cortical and white matter maturation in infants using complementary multi-modal imaging methods. The team research is focused on the cerebral bases of cogniti

[Freesurfer] Measure outer surface area

Dear all, how can I measure the surface area of the outer surface computed to calculate lgi? I've tried mris_anatomical_stats subject lh pial-outer-smoothed but that doesn't work (since it doesn't match lh.pial). Any idea would be greatly appreciated. T

Re: [Freesurfer] Inter-hemispheric registration issue

Dear Doug, thanks for putting mri_vol2vol on the ftp site, and sorry for bothering you again with this. I did as suggested, but I still get an error, now when attempting to run xhemireg. Apparently nu.mgz is missing. Please find the log attached. Thank you very much again, Irene Le vendredi

Re: [Freesurfer] Inter-hemispheric registration issue

nu.mgz does not exist Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 x86_64 GNU/Linux recon-all -s ac_copie/xhemi exited with ERRORS at Tue May 29 18:24:26 CEST 2012 Should I skip that by using the --no-tal flag? Thanks! Irene Le samedi 02 juin 2012 à 10:57 -0400, Douglas Greve

[Freesurfer] ROI from left to right hemi - cortical thickness

hen I tried to run mris_anatomical_stats on /subject/xhemi it failed, as there is no wm.mgz file in /subject/xhemi/mri. Any suggestion would be greatly appreciated. Thank you, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue

[Freesurfer] ROI from left to right hemi - cortical thickness

hen I tried to run mris_anatomical_stats on /subject/xhemi it failed, as there is no wm.mgz file in /subject/xhemi/mri. Any suggestion would be greatly appreciated. Thank you, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue

Re: [Freesurfer] ROI from left to right hemi - cortical thickness

/lh.mylabel.label --trglabel $SUBJECT_DIR/suj1/xhemi/label/lh.mylabel.label --regmethod surface --surfreg sphere --hemi lh 2) copy the newly created label /suj1/xhemi/label/lh.mylabel.label to suj1/label/rh.mylabel.label and calculate stats from that one? Thanks again! Have a nice day, Irene Le lundi 16

[Freesurfer] intrinsic curvature

Hi FS Developers,I would like to know if the measures of intrinsic curvature of FS are quite reliable; I would like to launch a project with this parameter, but I've never used this.Which is your experience? Thanks,IreneResident in Neurology, Italy ___

[Freesurfer] cortical thickness asymmetries

Dear Freesurfer experts, have cortical thickness asymmetries ever been looked at using Destrieux parcellation scheme, either in adults or (even better) in children? Thanks! Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue

Re: [Freesurfer] Longitudinal pipeline question

, Irene Le jeudi 03 novembre 2011 à 10:40 -0400, Martin Reuter a écrit : > Hi Irene, > > both images should be smoothed the same. You only have two time points > in each subject? Which FreeSurfer version are you using? And these > images are from the *.long.base directories (or ar

Re: [Freesurfer] different interpolation smoothing in conform step

Dear Martin, the RAS coordinates and voxel to ras transforms are indeed slightly different. Should I change this and if so, how? Please find the output of mri_info for each of the two acquisitions at the end of this email. Thanks again! Irene

Re: [Freesurfer] different interpolation smoothing in conform step

other suggestions... Thanks very much again for your help, Irene $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.22469/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (-0.0436194, 0, 0.999048) k_ras = (0.999048, 0

[Freesurfer] Postdoc position in neuroanatomical MRI of developmental dyslexia

Applications are invited for a postdoc position in the team of Franck Ramus, LSCP, Institut d'Etudes Cognitives, Ecole Normale Supérieure, Paris, France. The successful candidate will investigate neuroanatomical differences between dyslexic and control children, using high-quality 3T MRI images f

[Freesurfer] Inter-hemispheric registration issue

find /path/subject/xhemi/label/lh.aparc.annot lh.fsaverage_sym.sphere.reg is created in $subject as it should (please find the surfreg log below). Thank you in advance, Irene Log file for surfreg samedi 12 mai 2012, 17:36:31 (UTC+0200) setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ cd

Re: [Freesurfer] Inter-hemispheric registration issue

2012/01/20 20:12:32. Should that --keep-precision option be removed from the script? Thank you, Irene Le mercredi 16 mai 2012 à 11:16 -0400, Douglas N Greve a écrit : > Irene, this is a problem with the script. The work-around is to run > xhemireg before running surfreg with the --x

[Freesurfer] cortical lesions with FS (T1+DIR sequences)

msec, delay = 325 msec, echo train length (ETL) = 17, 50 contiguous axial slices with a thickness = 3 mm, a matrix size = 130 x 256, and a field of view (FOV) = 250 x 200 mm. Thanks, Irene Mattisi Multiple Sclerosis Centre Padua, Italy ___ Frees

[Freesurfer] differences between last and new version of FS

n of FS I could obtain about 80 cortices. So, can I obtain 80 cortices also with the new version of FS? How can I do it? Thanks Irene Mattisi Centre of Multiple Sclerosis, Hospital of Padova, Italy___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

[Freesurfer] (no subject)

Hi everybody, I would like to know if with the new version of FS I can also obtain the cerebellar cortical volume. Thanks Irene Mattisi Multiple Sclerosis Centre of Padua, Italy___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] (no subject)

find the entries in the aseg. stats file? Thanks!! Irene Mattisi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] cerebellar cortical volume

tain these measures? Thanks, Irene Mattisi___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] White matter hypointensities

. Thanks very much in advance, Irene Le mercredi 12 mai 2010 à 20:06 -0400, Bruce Fischl a écrit : > Hi Victor > > we treat it as any other label - it's manually labeled in the training > subjects and propagated into the aseg. Koen Van Leemput (ccd) has some > tools for segmen

[Freesurfer] problem with labels

shifted. Am I missing something? Should I use mri_label2vol or some other command? Thanks very much in advance! Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32

Re: [Freesurfer] Visualizing SPM Results on Template FreeSurfer Brain

Would it be wrong to overlay the activations (spmT.img maps) on fsaverage, convert them into labels (through Fill Stats) and use label2label to map them to each subject's surface? Thanks very much! Irene Le mardi 15 mars 2011 à 16:08 -0400, Douglas N Greve a écrit : > After you

[Freesurfer] flipping left-right

good? Thanks very much for your help! Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32 26 23 ___ Freesurfer mailing list Freesurfer@nmr.mgh.h

[Freesurfer] comparing FS version 4.0 and FS versione 5.2

Hi all, I'm performing a follow-up longitudinal study in a group of patients. I have 2 brain MRIs per patient (T0 and T1 after 4 years). I'd like to know if I can analyse the T0 MRI with FS version 4.0 and compare these results with T1 MRI analyzed with FS version 5.2. Thanks, Ire

[Freesurfer] Wm segmentation problem

attached picture. This concerns most of the coronal slices. We have been checking that control points were not misplaced and they look ok to us. What do you think is happening there and is there anything we can try before manually correcting these errors? Thanks very much in advance, Irene

Re: [Freesurfer] Wm segmentation problem

Dear Khoa and Bruce, thanks for replying so fast. The wm.mgz does not look correct either. I have uploaded the subject using the second option. Thanks again, Irene Le lundi 06 juin 2011 à 07:46 -0400, Khoa Nguyen a écrit : > Hi Irene, > > Is the wm segmentation correct in the wm.mg

[Freesurfer] recon all with optiBET brain mask

surface errors for the majority of them and that is why we would like to implement the optiBET mask. Thanks for your help, Irene Balboni PhD student She/Her Institute de plurilinguisme<https://secure-web.cisco.com/1pftPU5_0h0FupMF_jZDy_UxBYrJAQ-AW89umP7RzP_duHGk4rhiIzM9LB0z7YfOSEvpcpUW2V

Re: [Freesurfer] recon all with optiBET brain mask

segmentation and we have the skull-stripped images only for one of them so the solution below might not be ideal. Thanks again. Best, Irene From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: venerdì 29 dicembre 2023 15:44 To: Freesurfer support list Subject: Re