[Freesurfer] Fwd: Regarding: mris_label2annot

Dear Freesurfer experts, I am trying to create medial temporal lobe and for that I ran the command mri_annotation2label to create ?h.entorhinal.label, ?h.temporalpole.label and ?h.parahippocampal.label from fsaverage and stored these labels in labels.?h directory. After this I ran mris_label2annot

Re: [Freesurfer] CUDA in FS6?

On 2 February 2017 at 22:58, Chris Adamson wrote: > I have tested a recon-all -all CPU and GPU with and without the -hires option > and everything seems to run fine. So at the moment they seem to be compatible > or at least the GPU version doesn't crash. So that is ok. If you do come across sub

[Freesurfer] Surface based analysis for hippocampus subfield thickness

Dear all, Is there any approach that you recommend to quantify that changes in cortical thickness in hippo campus sub fields , how could i perform Surface based cortical thickness changes using freesurfer. Thanks Vasudev ___ Freesurfer mailing list Fre

[Freesurfer] Perirhinal 6.0 error

Hi, by running the mri_label2label to calculate perirhinal morphometry the following error occurs with FS6.0ERROR reading sub_DIR/label/rh.perirhinal.label Thanks Stefano___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.har

Re: [Freesurfer] license file not working

Hello, I got it running. I just deleted all old license files, resent the the registration. When I got the email I created both a .license and a license.txt in $Freesurfer_Home, and it worked. Just one of those things I guess? Anthony On 2/3/17 12:34 PM, Z K wrote: > Anthony, > > Is this sti

Re: [Freesurfer] Probability Maps

no, more like: echo "mri_normalize -b 20" > x.opts recon-all -s subjectID -autorecon2-cp -autorecon3 -expert x.opts or if you ware starting from scratch, use your command with the -expert x.opts stuff at the end cheers Bruce On Fri, 3 Feb 2017, Pascal Goodman wrote: Thanks bruce. That's

Re: [Freesurfer] Probability Maps

Thanks bruce. That's Line 1 recon-all -all -i T2 T2pial -s subjectID -parallel Line 2 mri_normalize -mprage -norm2-b 20 -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz This is in visual studio code Cheers, Pascal On Fri, Feb 3, 2017 at 3:45 PM, Bruce Fischl wrote: > Hi Pascal

Re: [Freesurfer] Probability Maps

Hi Pascal you can put the mri_normalize -b 20 line in a file, and use it as the expert options in recon-all to rerun autorecon2-cp and autorecon3 with it cheers Bruce On Fri, 3 Feb 2017, Pascal Goodman wrote: Thanks bruce. After running mri_normalize -mprage -b 20 -aseg aseg.presurf.mgz

Re: [Freesurfer] Probability Maps

yes On Fri, 3 Feb 2017, Pascal Goodman wrote: Also Bruce, Can I use this command line for the new version of freesurfer "  mri_normalize -mprage -norm2-b 20 -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz". ThanksPascal.  On Fri, Feb 3, 2017 at 2:47 PM, Pascal Goodman wrote:

Re: [Freesurfer] Probability Maps

Also Bruce, Can I use this command line for the new version of freesurfer " mri_normalize -mprage -norm2-b 20 -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz". Thanks Pascal. On Fri, Feb 3, 2017 at 2:47 PM, Pascal Goodman wrote: > Thanks bruce. After running mri_normalize -mprage -

Re: [Freesurfer] Probability Maps

Thanks bruce. After running mri_normalize -mprage -b 20 -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz, do I need to run recon-all -autorecon2 -autorecon3 again? Cheer., Pascal On Fri, Feb 3, 2017 at 2:38 PM, Bruce Fischl wrote: > Hi Pascal > > yes, that is the right command line.

Re: [Freesurfer] Probability Maps

Hi Pascal yes, that is the right command line. I don't know if you will need more control points, but that helped a lot. -a specifies the intensity threshold above 110 and -g specifies the spatial gradient for the 1d normalization cheers Bruce On Fri, 3 Feb 2017, Pascal Goodman wrote: Hel

[Freesurfer] Whole brain mediation analysis

Hi, I was wondering if you guys had any suggestions for developing a whole brain mediation analysis through Freesurfer or can think of any examples (e.g., does thickness mediate the relationship between age and cognition)? It looks like SPM has something (whole brain mediation analysis), and give

Re: [Freesurfer] Probability Maps

Hello Bruce, Thank you very much. a) The mri_normalization command line is where control points starts (normalization2). Right? b) Also, is this right command " mri_normalize -mprage -b 20 -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz

Re: [Freesurfer] Probability Maps

HI Pascal I got significantly improved results using -b 20 on the mri_normalize command line. Note that this has to come after the mprage. I think you can do it with an expert options file with: mri_normalize -b 20 cheers Bruce On Fri, 3 Feb 2017, Pascal Goodman wrote: Hello Bruce, I sent

Re: [Freesurfer] Kind Request - Trouble with FreeSurfer LICENSE file

The LICENSE file contained in the freesurfer release is a Software License Agreement and has nothing to do with the license file required to run the freesurfer program. To get a license file, please go to our registration page and a license will be emailed to you. Just copy the correct portion

[Freesurfer] Kind Request - Trouble with FreeSurfer LICENSE file

To Whom It May Concern: I am currently unable to successfuly register my copy of FreeSurfer with the license keys I received. Although I found a LICENSE file in the FreeSurfer program directory after successfully installing the program, I could not find the CUT Here lines as well as the locatio

Re: [Freesurfer] license file not working

No worries Bruce! Matt. On 2/3/17, 12:52 PM, "Bruce Fischl" wrote: >Hi Matt > >just to clarify - our old license format stopped working with newer >versions of libcrypt and so we were forced to change to the new format. >It >was not done gratuitously on our part or as a way to get people to >r

Re: [Freesurfer] license file not working

Hi Matt just to clarify - our old license format stopped working with newer versions of libcrypt and so we were forced to change to the new format. It was not done gratuitously on our part or as a way to get people to request new licenses - we had no choice. cheers Bruce On Thu, 2 Feb 2017

Re: [Freesurfer] Probability Maps

Hello Bruce, I sent it. Pascal On Fri, Feb 3, 2017 at 11:26 AM, Bruce Fischl wrote: > https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > > tar and gzip an example subject directory and send us the voxel coords of > points you want us to look at > > > cheers > Bruce > On Fri, 3 Feb 2017,

[Freesurfer] A note about the Freesurfer license file

Hello All, Users on newer linux distributions who upgrade from Freesurfer version 5.3 to version 6.0 may get the following error message: -- GNU libc version: 2.17 ERROR: Systems running GNU glibc version greater than 2.15

Re: [Freesurfer] license file not working

Anthony, Is this still an issue for you? So long as there is a license file (name .license or license.txt) in the FREESURFER_HOME directory, you should be all set. -Zeke On 02/02/2017 06:46 PM, Anthony Dick wrote: > Thanks Matt. I already tried it with a new registration, but it doesn't > hurt

Re: [Freesurfer] Multiple comparison question

Thank you, Anderson. Regards. VM On Thu, Feb 2, 2017 at 11:06 PM, Anderson M. Winkler wrote: > Hi VM, > > They can stay all in the same .csv file. The "fwep" files will have > p-values corrected across all columns of this input. > > All the best, > > Anderson > > > On 2 February 2017 at 12:09,

Re: [Freesurfer] how to export cortical thickness in to .txt

Hi shi yao if you have run recon-all then we have already done this for you. Look in the subject's stats dir (that is, $SUBJECTS_DIR/$subject/stats) cheers Bruce On Fri, 3 Feb 2017, shi yao wang wrote: Dear Fs experts:I would like to use mris_anatomical_stats to calculate 35 cortical

[Freesurfer] how to export cortical thickness in to .txt

Dear Fs experts: I would like to use mris_anatomical_stats to calculate 35 cortical regions thickness. I am using following command: mris_anatomical_stats -a subjid/label/lh.aparc.annot -b subjid lh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] how to export cortical thickness in to .txt

Sorry for the interrupted. My question is how to export the results to .txt files. I found that there is a -f argument, however it doesnot work. thanks Shiyao On Fri, Feb 3, 2017 at 11:41 AM, shi yao wang wrote: > Dear Fs experts: > I would like to use mris_anatomical_stats to calculate 35 cort

Re: [Freesurfer] Probability Maps

Thanks bruce. Do I upload the entire file? Also,where can I find the link? Pascal On Fri, Feb 3, 2017 at 10:35 AM, Bruce Fischl wrote: > Hi Pascal > > I don't think tissue priors will help due to the complexity and > variability of the folding patterns. There may be other interventions > though

Re: [Freesurfer] Probability Maps

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange tar and gzip an example subject directory and send us the voxel coords of points you want us to look at cheers Bruce On Fri, 3 Feb 2017, Pascal Goodman wrote: Thanks bruce. Do I upload the entire file? Also,where can I find the link

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

Thanks for the clarification Eugenio, Much appreciated Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: 03 February 2017 15:59 To: Freesurfer support list Subject: Re: [Freesurfer]

Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs (REPOST)

Hey Lilla, I found the error that I made in the original command I posted; I forgot to switch the --targ & --mov inputs in the first mri_vol2vol command. Here's the corrected version that works for me: mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUB

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

Hi! recon-all -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair looks good. The flag -hippocampal-subfields-T1FLAIR does not even exist ;-) Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http

Re: [Freesurfer] Probability Maps

Hi Pascal I don't think tissue priors will help due to the complexity and variability of the folding patterns. There may be other interventions though - can you send us some examples of where things don't look accurate to you? cheers Bruce On Fri, 3 Feb 2017, Pascal Goodman wrote: Hell

Re: [Freesurfer] Probability Maps

Hello Bruce, Thanks for replying. I am trying find ways to improve white matter surface (to reduce manual intervention by control points) with the probability map. Also, how do I extract the multiple prior maps you mentioned. Thank you. Best, Pascal On Fri, Feb 3, 2017 at 10:22 AM, Bruce Fischl w

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

Thanks Bruce, Much appreciated Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 03 February 2017 15:18 To: Freesurfer support list Subjec

Re: [Freesurfer] Probability Maps

Hi Pascal what are you trying to achieve? Internally we have multiple prior maps of this type, but I don't think we are setup for a user to supply a different one cheers Bruce On Fri, 3 Feb 2017, Pascal Goodman wrote: Hello Freesurfer, I do have a question. Can FS take probability maps of

Re: [Freesurfer] possible atlas error to report

Hi Jacob the unthresholded BA44 spreads over a lot of prefrontal cortex as low probability but possible locations for 44. Using it confounds variability with size. cheers Bruce On Fri, 3 Feb 2017, Levman, Jacob wrote: The following pair are consistent: lh.BA.thresh BA44 GrayVol rh.BA.thre

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

Hi Erik Eugenio can confirm, but I don't think the subfield stuff cares. The -hippocampal-subfields-T1T2 means use multiple inputs, but it doesn't assume anything about the distribution of intensities in them. cheers Bruce On Fri, 3 Feb 2017, Erik O'Hanlon wrote: Hi Experts, Just flowing

Re: [Freesurfer] Specification of computer

Hi Aziz with multiple course you can specify -openmp 8 for exmaple to use 8 cores, which speeds things up a lot. It also depends how many recons you will be running at the same time. A 16 core machine with 64G of ram would be able to run 4 recons in a few hours each. cheers Bruce On Fri, 3

[Freesurfer] [FSFAST] Matlab parallel

Hi all, So this is a question about running FAST through matlab parallel desktop: I know it is very funny (and inefficient) because I open up a bash in the matlab to run a csh script that generates and runs a matlab code, but just I’m familiar with matlab in doing many things including string m

[Freesurfer] Contrast percent map

Hi Doug, Thank you so much for clarification. Probably there is an issue with the mailing list, I only received the digest list, and now I saw your reply. In fact, I found it by myself while looking through fast_selxavg3.m: the baseline being defined by the overall offset. and yes, I was thinki

[Freesurfer] Probability Maps

Hello Freesurfer, I do have a question. Can FS take probability maps of tissue segmentation as prior? Thanks, Pascal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

Re: [Freesurfer] possible atlas error to report

The following pair are consistent: lh.BA.thresh BA44 GrayVol rh.BA.thresh BA44 GrayVol The following pair are inconsistent: lh.BA BA44 GrayVol rh.BA BA44 GrayVol Other measurements in the lh.BA and rh.BA atlases may also be inconsistent. Thanks, Jacob Fro

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

Hi Experts, Just flowing on from Joe's question, I have run my analysis without the T2 or FLAIR flag but have specificed the T2 which is a FLAIR image for the hippocampal subfield options. I have used recon-all  -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_008_T2.nii.gz T2Flair

[Freesurfer] Specification of computer

Hi experts, I would like to find a new high-performance computer to run the reconstruction process in Freesurfer. Currently, I used a single computer (Intel core i7, RAM 8MB) to run the commands (e.g., 'recon-all -all' ) that spent average time 7-9 hours per one subject data. Please let me know

Re: [Freesurfer] extract values uncorrected clusters

Hi Doug, thanks for your reply. I'm trying it out but I get this error message: ERROR: srcsubjid must be supplied I have 40 subjects in 2 groups. What exactly do I enter as --subject ? Thanks for your help! Clara - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.ha

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

Thanks for the quick reply. I'll re-run my subjects with the -FLAIR flag. Joe From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 02 February 2017 22:56 To: Freesurfer support list Subject: Re: [Freesurfer] Simple question regarding

Re: [Freesurfer] How to check recon-all finished without any error

Dear Emroy, I can also recommend using QA tools: https://surfer.nmr.mgh.harvard.edu/fswiki/QATools You can edit the "default_status_log_xx" files in the folder and enter the steps that you're interested in. Give it a try. Kind regards, Sebastian - Original Message - From: "Trisanna Sp

[Freesurfer] Regarding: mris_label2annot

Dear freesurfer experts, I am trying to create medial temporal lobe and for that I ran the command mri_annotation2label to create ?h.entorhinal.label, ?h.temporalpole.label and ?h.parahippocampal.label from fsaverage and stored these labels in labels.?h directory. After this I ran mris_label2annot

[Freesurfer] Fw: Analysis of rates or percent changes

Hi Martin, Apologies for multiple e-mails, but I got a message that something might be wrong with the previous e-mail, so I forward it again. Please find below my previous question. Regards, Katarina Katarina Trojacanec, M.Sc. Teaching and research assistant Faculty of Computer Science an