[Freesurfer] strange error in lme_mass_RgGrow

External Email - Use Caution When I run lme_mass_RgGrow on mgh using lme it wil fit 20 % before it quite. Is there a problem with my system? Region 4450: Convergence at iteration 3. Initial and final likelihoods: 473.1215, 473.7587. Aproximate percentage of fitted locations: 20

Re: [Freesurfer] Editing Issues

External Email - Use Caution Hi Jocelyn, Many thanks for your response. I just wanted to confirm a couple of things: 1. Could you advise what specific edits need to be made to the brainmask.mgz volume to fix the hole in the WM, i.e., do we need to add GM, delete GM? We are used

Re: [Freesurfer] mri_glmfit_sim error (Douglas N. Greve)

The FWHM 38 values is the final smoothness that includes applied and inherent. with lGI, you get a lot of inherent smoothing. You can try not smoothing at all, but I would probably go for permutation rather than MCZ On 11/5/2020 12:39 PM, Basavaraju, Rakshathi wrote: > External Email -

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed}

Sorry, try this mri_segstats --i qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.areapial.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_areapial.avgwf.dat (output file) --accumulate --sum lh_areapial.sum (output file)

Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC {Disarmed}

The caudate segmentation would not affect the surface placement. Is the surface placement ok? Can you send a pic of the caudate error? On 11/6/2020 9:58 AM, Donatienne Van Weehaeghe wrote: External Email - Use Caution Dear, Would there be another option to fix this? Kind regards Don

Re: [Freesurfer] mris_anatomical_stats error: stating file

Can you send the exact command line that generated the terminal output you sent? The line below has a different subject name. Run that command from the shell (rather than from your script) to verify that it creates an error On 11/5/2020 11:29 AM, Chan, Shi Yu wrote: Hi, Yes, sorry! I copied

Re: [Freesurfer] please help me {Disarmed}

Also, when you use --subjects, just supply the subject name (subj1), not a path to the subject On 11/6/2020 11:56 AM, Ammon, William wrote: Hello, Are you still getting the error message that “atleast 1 subject must be provided”? Or is it a different error message? The screenshot shows you

Re: [Freesurfer] Fixed factor vs nuisance factor

Nuisance On 11/8/2020 7:42 AM, Sunil Khokhar wrote: External Email - Use Caution Dear Experts, In QDEC, to which box should the categorical variables like gender should go to, given that gender is a variable of no interest? Should it be fixed factors box or the nuisance factors box?

Re: [Freesurfer] question about ventricular volume calculation

The creation of the aseg (mri_ca_label) mainly defines the ventricle segmentation, then  the volume is computed by mri_segstats. The calculations for ventricular and subcort volume are done in the same way by mri_segstas On 11/8/2020 6:11 AM, Jiao Qing wrote: External Email - Use Cau

Re: [Freesurfer] mri_vol2vol usage

Try --help to get docs and examples On 11/8/2020 5:07 PM, RENXI LI wrote: > External Email - Use Caution > > Hi FreeSurfer Experts: > > I am trying to register the subject’s functional image processed by SPM12 to > the Freesurfer subject anatomical space using mri_vol2vol, what would be

Re: [Freesurfer] Create new .mgz from .annot

On 11/9/2020 3:58 PM, Hyon, Justin J. wrote: > External Email - Use Caution > > Hello, > > I’m new to Freesurfer and am trying to learn the steps to manually label some > brain regions for use in source localization in MNE. So far my understanding > is that I have to create label files

Re: [Freesurfer] Correlation between thickness and csf_measures: vector

On 11/10/2020 5:36 AM, Steve Petersen wrote: External Email - Use Caution Dear Freesurfer experts, I am conducting a cortical thickness study in three groups. After performing the between-group analyses, I would like to evaluate the possible correlation between cortical thickness

Re: [Freesurfer] color and sign of sig.mgh data

On 11/10/2020 8:25 AM, Rovai Antonin wrote: > External Email - Use Caution > > Hello, > > I am creating sig.mgh overlays in a group analysis. On this map, I can > see some blue and red vertices, corresponding to negative and positive > values (respectively) on the map. > > On the other h

Re: [Freesurfer] question about ventricular volume calculation

The volume comes from the whole brain segmentation (aseg.mgz, see Fischl, 2002, Neuron paper). On 11/10/2020 7:46 PM, Jiao Qing wrote: External Email - Use Caution Dear FreeSurfer Developers: I want to calculate ventricular volume using the 'recon-all' procedure. Would you like to l

[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

Re: [Freesurfer] Editing Issues

Hi Harriet Do you know that it is a hole? More likely is that it only looks like one on a single slice and if you scroll back and forth or change to a different view you will find that it is not actually a hole. As for the second question you only need to edit things if the nearby surfaces are

Re: [Freesurfer] Help with mergecontrasts-sess function

There is not a summary table, it is just a map. Do you want a cluster table? On 11/10/2020 11:26 AM, Paula Maldonado wrote: External Email - Use Caution Thanks for your reply, that worked. Can you please tell me where I can find a summary table of the activated regions resulting from

Re: [Freesurfer] Recon1 command {Disarmed}

I think you can still do what Bruce suggested and keep things separate. What's the problem? On 11/10/2020 1:11 PM, Kelli Ann Nini wrote: External Email - Use Caution Dr. Fischl, Thank you so much for your reply. The brains I'm using have been processed and analyzed numerous times for

Re: [Freesurfer] Help with mergecontrasts-sess function {Disarmed}

External Email - Use Caution Yes, please, Best regards, Paula > Il giorno 11 nov 2020, alle ore 17:32, Douglas N. Greve > ha scritto: > > There is not a summary table, it is just a map. Do you want a cluster table? > > On 11/10/2020 11:26 AM, Paula Maldonado wrote: >>

Re: [Freesurfer] mris_anatomical_stats error: stating file

Hi, Sure, I've attached 2 txt files: fs_terminal_output.txt - I pasted the lines from the script into the command line for sub-230_ses-01 fs_terminal_output_short.txt - I just ran mris_anatomical_stats on the left hemisphere alone for sub-230_ses-01 I get the same error in both cases. I've t

Re: [Freesurfer] mri_vol2vol usage

Yes, use bbregister, run with --help to get docs On 11/11/2020 11:36 AM, RENXI LI wrote: > External Email - Use Caution > > So I think my functional image processed by SPM12 does not come with any > registration matrix file that is required for mri_vol2vol, is there a way to > get aroun

Re: [Freesurfer] mris_anatomical_stats error: stating file

Try giving it a full path the the annot, eg, -a $SUBJECTS_DIR/sub-230_ses-01/label/lh.Yeo2011_17Networks_N1000.annot On 11/11/2020 12:09 PM, Chan, Shi Yu wrote: Hi, Sure, I've attached 2 txt files: fs_terminal_output.txt - I pasted the lines from the script into the command line for sub-23

Re: [Freesurfer] Canon MRI morphometry protocols

Hello Shujiro, Our group has never used Canon scanners before, so unfortunately I don’t have any Canon-specific protocol I can point you to. Below is the link to our suggested T1 structural protocol as we have used/tested on Siemens scanners before. You could try to reproduce this protocol on y

Re: [Freesurfer] mris_anatomical_stats error: stating file

Hi, Thank you, that fixed the error! Also, I’m glad to say that the error didn’t make a difference in the output stats files. From: freesurfer-boun...@nmr.mgh.harvard.edu Date: Wednesday, November 11, 2020 at 12:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_anatomica

[Freesurfer] Flywheel is Hiring

External Email - Use Caution Hello Freesurfer and Neuroinformatics Experts, At Flywheel

Re: [Freesurfer] mri_vol2vol usage

External Email - Use Caution So I think my functional image processed by SPM12 does not come with any registration matrix file that is required for mri_vol2vol, is there a way to get around with that matrix? Best, Renxi > On Nov 11, 2020, at 10:12 AM, Douglas N. Greve wrote:

Re: [Freesurfer] mri_vol2vol usage

External Email - Use Caution Wouldn’t --reg still require the registration matrix file in bbregister? Best, Renxi On Nov 11, 2020, at 11:40 AM, Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: Yes, use bbregister, run with --help to get docs On 11/11/2020 11:36 AM, RE

Re: [Freesurfer] mri_vol2vol usage

No, that is the output of bbregister On 11/11/2020 1:55 PM, RENXI LI wrote: External Email - Use Caution Wouldn’t --reg still require the registration matrix file in bbregister? Best, Renxi On Nov 11, 2020, at 11:40 AM, Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: Ye

[Freesurfer] tkregister issue with reg-feat2anat {Disarmed}

External Email - Use Caution Greetings, I am experiencing a similar tkregister2 issue described in this thread when attempting to run reg-feat2anat: https://secure-web.cisco.com/1H9mU-9s00zN3P3mT0enoWLpI-9zwcO9lCds21sBQW9qoSPpMEcJ1KDcbQsvZ9iZ1Wu8IP-mx8SyKgy5jTrUhqaifkxwjnbydCn31