[Freesurfer] postdoc position at Karolinska Institutet (Sweden)

Do you want to contribute to top quality medical research? We are looking for a postdoctoral fellow for studies of brain degeneration in Lewy Body dementia (DLB) using advanced brain imaging methods. ki.varbi.com All the best Dani -- Daniel Ferreira, PhD, Docent (Associate Professor) Director of Center f

Re: [Freesurfer] Talairach Transform failure

nput data to make sure that > something is not really wrong. Eg, a large artifact or unusual anatomy. > > On 1/17/19 5:35 AM, Daniel Ferreira wrote: > > > > External Email - Use Caution > > > > Thanks Greve. Yes, I mean that the moveable is completely

Re: [Freesurfer] Talairach Transform failure

f view > > On 1/16/19 11:30 AM, Daniel Ferreira wrote: > > > > External Email - Use Caution > > > > Hi Greve, > > > > Thanks for your quick reply. > > > > I mean that tkregister2 loads the target volume (I think the original >

Re: [Freesurfer] Talairach Transform failure

at do you mean that the tal volume does not load as a mov volume? Can > you send the terminal output from tkregister2? > > On 1/16/19 10:01 AM, Daniel Ferreira wrote: > > External Email - Use Caution > > Dear Bruce, Martin, and experts, > > > I posted an issue a

[Freesurfer] Talairach Transform failure

? Thank you very much in advance Dani Daniel Ferreira <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Daniel+Ferreira%22> Wed, 09 Jan 2019 10:22:05 -0800 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20190109> Ex

[Freesurfer] Talairach Transform failure

s wondering if you would know about any way to fix this? Thank you in advance, Dani -- *Daniel Ferreira, PhD, Assistant Professor* Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences and Society Karolinska Institutet (Sweden) *Address: **Blickagången 16, 141 52 Hudding

Re: [Freesurfer] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies

nd back again produces interpolation artefacts that are > significant and at orders comparable with 1 year of neurodegenerative > disease. > > Best, Martin > > > > > > On 30. Aug 2018, at 18:22, Daniel Ferreira wrote: > > > > Dear colleagues, > > I was

[Freesurfer] Is voxel size resampled during recon-all? And different voxel size in longitudinal studies

be performed by any way) that minimizes these differences in somehow. Thank you very much Dani -- *Daniel Ferreira, PhD, Assistant Professor* Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences and Society Karolinska Institutet (Sweden) *Address: **Blickagången 16, 141 52

Re: [Freesurfer] FreeSurfer on MP2RAGE

any opinion on which sequence to use? Thank you very much, Best regards Dani -- Daniel Ferreira, PhD. Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics (Karolinska Institute, Sweden) danif...@gmail.com | daniel.ferreira.padi...@ki.se 2016-09-28 10:15 GMT

[Freesurfer] FreeSurfer on MP2RAGE

have always produced nice results with the MPRAGE sequence and the MPRAGE flag seems to work well. Do you think this flag will work as well on MP2RAGE? Of course it is difficult to say but we wonder if you have any opinion on which sequence to use? Thank you very much, Best regards -- Daniel

[Freesurfer] -qcache of v5.0 data with newer versions

Dear experts, Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been recon-all -all with FS 5.0.0? Thanks Dani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

[Freesurfer] -qcache of v5.0 data with newer versions

Dear experts, Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been recon-all -all with FS 5.0.0? Thanks Dani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

[Freesurfer] using -cw256 as default is good?

Dear experts, Could you please help me with my previous comment (see below)? Thanks so much Daniel Ferreira Dear experts, We are processing a dataset that gives us this error quite often: ERROR! FOV=300.000 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head

[Freesurfer] using -cw256 as default is good?

Dear experts, We are processing a dataset that gives us this error quite often: ERROR! FOV=300.000 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. Is it ok if I use -cw256 by default to all my scans even for those with FOV=256 that do not need

Re: [Freesurfer] longitudinal processing, template and flags

it to the -base and -long runs, just to be safe. best, Martin On 01/29/2014 09:08 AM, Daniel Ferreira wrote: Dear experts, I have two questions regarding the longitudinal stream: - I am including Baseline and 12 months follow-up in my study. However, I also have 6 months follow-up. I wonder

[Freesurfer] longitudinal processing, template and flags

registration. - I am applying the -mprage flag in the crossectional first step. Should I use it in the -base and -longs steps too? Thanks very much Daniel Ferreira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] acquisition in 1 session vs 2 sessions

be affected by this issues. Thanks a lot. Daniel Ferreira ___ 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

[Freesurfer] Fwd: missing eTIV in asegstats2table

in the same email. I go through way too many emails to keep track of who's doing what. thanks! doug On 10/23/13 4:13 AM, Daniel Ferreira wrote: Dear Douglas, Please, find attached aseg.stats files for subj1 and subj2. Thanks Daniel Message: 4 Date: Tue, 08 Oct 2013 11:39:11 -0400 From

Re: [Freesurfer] missing eTIV in asegstats2table

Dear Douglas, Please, find attached aseg.stats files for subj1 and subj2. Thanks Daniel aseg.stats_subj2 Description: Binary data aseg.stats_suj1 Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] missing eTIV in asegstats2table

Dear Douglas, I generated my table with version 5.3. Attached is an example for two subjects (in .txt and .xls formats). Best regards Dani Measure:volume Left-Lateral-Ventricle Left-Inf-Lat-Vent Left-Cerebellum-White-MatterLeft-Cerebellum-Cortex Left-Thalamus-Proper

Re: [Freesurfer] missing eTIV in asegstats2table

Dear Douglas and Martin, Thanks for your replies. So far I have always been able to get eTIV when running asegstats2table (last column on the spreadsheet). But my current FreeSurfer version (5.3.0) is not grabbing it. I can found eTIV in the header and extract it for all the subjects with

Re: [Freesurfer] missing eTIV in asegstats2table

a lot Dani Message: 7 Date: Wed, 02 Oct 2013 10:32:51 -0300 From: Marcos Martins da Silva marc...@hucff.ufrj.br Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: Daniel Ferreira dani...@ull.es Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: 1380720771.1845.9.camel@alien Content-Type: text

Re: [Freesurfer] missing eTIV in asegstats2table

, eg the line now looks like # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1509814.835086, mm^3 On 10/01/2013 10:50 AM, Daniel Ferreira wrote: Hi, I just run my first asegstats2table in version 5.3 of FS. Is not eTIV included in the generated file anymore

[Freesurfer] missing eTIV in asegstats2table

Hi, I just run my first asegstats2table in version 5.3 of FS. Is not eTIV included in the generated file anymore? I know that I can get eTIV with mri_segstats --subject subjid --etiv-only but, is it any way to get the values for all my subjects in a text file as asegstas2table does? Thanks a

Re: [Freesurfer] average measure of cortical thickness

with the -m thickness option. This gives you a measure of mean thickness for the hemisphere as well. do8ug 2012/10/30 Daniel Ferreira dani...@ull.es Please, is there any automatic way to extract this Mean Thickness values for lh and rh for a big group of subjects? As for example aparcstats2table

Re: [Freesurfer] Talairach Failure Detection

. Nothing will work on this sorry Bruce On Tue, 23 Oct 2012, Daniel Ferreira wrote: Hi Nick, Here comes attached the tkmedit orig.mgz thanks Daniel 2012/10/22 Nick Schmansky ni...@nmr.mgh.harvard.edu what does orig.mgz look like in tkmedit? n. On Thu, 2012

Re: [Freesurfer] cortical parcellation question

sampling it into the volume (or just using the aparc+aseg.mgz that is distributed with fsaverage) cheers Bruce On Wed, 17 Oct 2012, Daniel Ferreira wrote: Hello again, Thanks for all the information Bruce. Is it not possible to back-project the regions defined in the 2D surface-based

[Freesurfer] average measure of cortical thickness

Hi, I was wondering what should I use as an average of cortical thickness for the whole cortex. The aparc.stats output gives a value of Mean Thickness for each hemisphere. But this value does not coincide with the one I get if I average the 34 variables from aparc.stats. Do you know why? thanks

Re: [Freesurfer] Talairach Failure Detection

Well, in the PACs looks fine. When converting to nii it is already wrapped. I will go to the machine again and see. Thanks! 2012/10/30 Bruce Fischl fis...@nmr.mgh.harvard.edu really? In what viewer? Does it happen in the rawavg.mgz? On Tue, 30 Oct 2012, Daniel Ferreira wrote: Hi, I

Re: [Freesurfer] average measure of cortical thickness

over the cortex. cheers Bruce On Tue, 30 Oct 2012, Daniel Ferreira wrote: Hi, I was wondering what should I use as an average of cortical thickness for the whole cortex. The aparc.stats output gives a value of Mean Thickness for each hemisphere. But this value does not coincide

Re: [Freesurfer] average measure of cortical thickness

Please, is there any automatic way to extract this Mean Thickness values for lh and rh for a big group of subjects? As for example aparcstats2table? thank you very much Daniel 2012/10/30 Bruce Fischl fis...@nmr.mgh.harvard.edu yes, I think so Bruce On Tue, 30 Oct 2012, Daniel Ferreira

Re: [Freesurfer] Talairach Failure Detection

Hi, I did recon-all -i dicoms -s id and then what Nick posted. 2012/10/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel what was your original data format? Did you start with dicoms? Bruce On Thu, 18 Oct 2012, Daniel Ferreira wrote: Thanks Nick very much for your suggestion

Re: [Freesurfer] cortical parcellation question

volume(s) and transformed (inflated) to the 2D spherical surface? Daniel -- Forwarded message -- From: Bruce Fischl fis...@nmr.mgh.harvard.edu Date: 2012/10/11 Subject: Re: [Freesurfer] cortical parcellation question To: Daniel Ferreira danif...@gmail.com Cc: freesurfer

[Freesurfer] cortical parcellation question

. are the neuroanatomical boundaries the same; does the left inferior temporal cortex in the Freesurfer cortical parcellation = the left inferior temporal cortex in the Harvard-Oxford atlas downloaded with FSL) Many thanks Daniel Ferreira ___ Freesurfer

Re: [Freesurfer] cortical parcellation question

. in the same format as the Harvard-Oxford atlas that is downloaded with FSL). Thanks a lot. Daniel Ferreira 2012/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Daniel, 1. Do you mean the atlas or the parcellation of your subjects? We cannot distribute the individual subjects in the atlas

[Freesurfer] Fwd: How TE, TI and flip angle parameters affect the images and results?

will have a big effect on dura (darkening it), but will also reduce gray/white contrast. cheers Bruce On Fri, 17 Aug 2012, Daniel Ferreira wrote: Dear all, We are designing a study based on clinical data. We want to work with a MPRAGE sequence but subjects have been given 4 different sets

[Freesurfer] How TE, TI and flip angle parameters affect the images and results?

: 9 - TR: 1900; TE: 3,39; TI: 900; flip angle: 15 I wonder how these differences could affect the images and thus the results. Can I combine all of them or at least some of them? Are they so different that I should just study them by separate? thank you very much on advance Daniel Ferreira

[Freesurfer] when are uncorrected 0, 001 results permitted instead of FWE?

results are justified or at least permitted instead of FWE? Any paper or information about this specific FWE disadvantages in aid of p0,001 uncorrected results? Thank you very much in advance Daniel Ferreira ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] Recon-all Error: _FindFacePath

Hello Khoa, Thank you very much for your suggestion. I checked both brainmask.mgz and wm.mgz and it saw ok for me. I have already sent my two scans to Bruce. Hope something can be done. Cheers! Daniel Ferreira 2011/9/13 Khoa Nguyen k...@nmr.mgh.harvard.edu Hi Daniel

Re: [Freesurfer] Recon-all Error: _FindFacePath

your scans to Bruce? Thanks, Fatima From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu [mailto: mailto:freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu]On Behalf Of Daniel Ferreira Padilla Sent: 14 September 2011 09:19

Re: [Freesurfer] Recon-all Error: _FindFacePath

Dear Bruce and experts, I would really appreciate if you can help me with my scans. I have successfully processed all my sample but got this same FindFacePath error with 2 subjects. I checked the brainmask and wm files and for me they look ok. So I do not know how can I fix this

Re: [Freesurfer] error while loading shared libraries:libtiff.so.3

have the permissions, prefix your ln command with a sudo and it'll ask for your password, and that should work successfully. If you don't have permissions, you need to ask your system administrator to do so. -Krish On Jun 20, 2011, at 5:44 AM, Daniel Ferreira Padilla wrote: Dear all, I'm

Re: [Freesurfer] error while loading shared libraries:libtiff.so.3

permission? Thank you very much for your help. Daniel Ferreira # #@# Cortical ribbon mask Sat Jun 18 17:57:36 WEST 2011 /home/neuroimagen/DANI/subjects/uu0148_36_1/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41

[Freesurfer] issues about pial and wm edit

separately? Can I do it at the same time? And if I could, what command do I have to use? I hope these are not too much questions. Thank you very much in advance. Daniel Ferreira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] tksurfer error

...@nmr.mgh.harvard.edu] Enviado el: miércoles, 10 de febrero de 2010 15:49 Para: Daniel Ferreira Padilla CC: freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] tksurfer error have you tried clicking the redraw button? On Wed, 10 Feb 2010, Daniel Ferreira Padilla wrote: Dear Freesurfer users, I