[Freesurfer] The input for FreeSurfer

External Email - Use Caution Hello Freesurfer developers, I have T1 weighted MRI images which are* not MPRAGE*. They are 2 dimensional sagittal or axial images with 3mm thickness (1.5 Tesla). Can I analyze these images by FreeSurfer? If yes, what tips should I consider? Thank

Re: [Freesurfer] nu_correct error

What version are you running? Can you send the recon-all.log file? On 7/16/2020 3:40 PM, Bahrani, Ahmed A. wrote: External Email - Use Caution Hello Freesurfer experts, I have a question related to the singularity container to run a bash script that contains a freesurfer's commend "n

Re: [Freesurfer] The input for FreeSurfer

You can't get accurate surfaces from that, but the volumetric segmentation might be ok On 7/17/2020 8:22 AM, Hengameh Marzbani wrote: External Email - Use Caution Hello Freesurfer developers, I have T1 weighted MRI images which are*not MPRAGE*. They are 2 dimensional sagittal or axia

Re: [Freesurfer] Flag(s) for parallel processing

-parallel -openmp 4 should run things with 4 processors and parallelize across hemi where it can The run time on that page is probably not accurate. But is it faster when you use those options? On 7/16/2020 11:47 PM, Billah, Tashrif wrote: This

[Freesurfer] Cortical Parcellations in FreeDurger 7

External Email - Use Caution Dear Freesurfer Developers, I hope this email finds you all safe and well. I have two questions regarding the new version of freesurfer: - Is there a new CLUT associated with FS7? I tried to use the CLUT labels to extract thalamic subnuclei ROI

Re: [Freesurfer] error in longitudinal stream fs7.1 ERROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! worked in fs6

I think you might have found a bug when a cross subject has more than one input. Can you download https://gate.nmr.mgh.harvard.edu/safelinks/greve/longmc Copy it to $FREESURFER/bin (make a copy of the one that is there) Then re-run? thanks On 7/16/2020 11:57 AM, Knut J Bjuland wrote:

Re: [Freesurfer] Cortical Parcellations in FreeDurger 7

On 7/17/2020 10:25 AM, Al Qadi, Ameen wrote: External Email - Use Caution Dear Freesurfer Developers, I hope this email finds you all safe and well. I have two questions regarding the new version of freesurfer: * Is there a new CLUT associated with FS7? I tried to use the CLUT

Re: [Freesurfer] The input for FreeSurfer

Hi Hengameh You can try, but 3mm may be too thick for accurate surface models. Once you have too many voxels that contain both sides of a sulcus it is difficult to recover accurate surfaces. Note that our inputs don’t have to be mprage, but 3D acquisitions are highly recommended Cheers Bruce

Re: [Freesurfer] ROI-wide cortical thickness for each network !

Try something like mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.yeo.stats -b -a ../label/lh.yeo.annot -c ../label/yeo.annot.ctab 1040 lh white Assuming that your yeo atlas is in $SUBJECTS_DIR/$subject/label/lh.yeo.annot On 7/15/2020 2:05 PM, Martin Juneja

Re: [Freesurfer] Extracting PET Binding Values from Inflated Surface

Yes, you can use mri_segstats. Run it with --help and see Example 6, change thickness to your BPND overlay On 7/15/2020 11:39 AM, O'Dell, Ryan wrote: External Email - Use Caution Hi Doug, I have a question surrounding our attempts to extract PET binding values (BPND/DVR) which have

[Freesurfer] Fwd: Fwd: question regarding mri_vol2label

External Email - Use Caution Hi FS team, I was wondering if you could take a look at the question below. Thanks! -- Forwarded message - From: Julie Ottoy Date: Fri, 10 Jul 2020 at 20:49 Subject: Re: [Freesurfer] Fwd: question regarding mri_vol2label To: Freesurfe

Re: [Freesurfer] Fwd: Fwd: question regarding mri_vol2label

External Email - Use Caution There is no tool (I know of) which does exactly what you want, but it should be easy in Matlab or R. So if I understand correctly you have several label files for one subject, and you want to apply all of them and get a single text file that should h

Re: [Freesurfer] Fwd: Fwd: question regarding mri_vol2label

Hi Julie I don’t think we have anything that will do this out-of-the-box, but it should be easy enough to do in matlab or python. The label files are a text format and we provide .m and .py files to read them. Alternatively you could combine all the labels into a single parcellation file /subje

Re: [Freesurfer] Fwd: question regarding mri_vol2label

Try mri_convert parcellationvolumes.mgz --ascii parcellationvolumes.txt On 7/10/2020 8:49 PM, Julie Ottoy wrote: External Email - Use Caution Thank you for your reply. It worked to convert to surface label :) When i overlay the surface labels on the pial surface, I can view a histo

[Freesurfer] rtview - loading a tcl file

Hi Surfers, I was wondering if there is a way to load a tcl file with rtview command. Specifically, I need to change the color table to RYGB, remove the aparc, ... . Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr

Re: [Freesurfer] rtview - loading a tcl file

I just added --tcl to rtview. The new version is in dev On 7/17/2020 12:23 PM, Nasr, Shahin,Ph.D. wrote: Hi Surfers,     I was wondering if there is a way to load a tcl file with rtview command.  Specifically, I need to change the color table to RYGB, remove the aparc, ... . Thanks

Re: [Freesurfer] rtview - loading a tcl file

Thanks. But as far as I see,when I use --tcl , it avoids execution of other tcl files such as eccen-flat.tcl. What I had in my mind was "adding" a tcl. Sorry for all the troubles From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent

Re: [Freesurfer] rtview - loading a tcl file

ok, try now On 7/17/2020 12:49 PM, Nasr, Shahin,Ph.D. wrote: Thanks. But as far as I see,when I use --tcl , it avoids execution of other tcl files such as eccen-flat.tcl. What I had in my mind was "adding" a tcl. Sorry for all the troubles -

[Freesurfer] FreeSurfer 7.1 patch question

External Email - Use Caution Hi FreeSurfer Experts, Is there a tentative date when the FreeSurfer 7.1 patch and docker implementation is going to be released? Thanks! Aylin _ Aylin Dincer Senior Research Technician NeuroImaging Laboratories Imaging C

Re: [Freesurfer] mri_fieldsign error

I was not able to replicate this on my CentOS7 linux box. You sent me left hemi data, so I ran the command below mri_fieldsign --fs fieldsign.71.nii.gz --polar LOO.wedge.polar.lh.real.nii.gz LOO.wedge.polar.lh.imag.nii.gz --eccen LOO.ring.eccen.lh.real.nii.gz LOO.ring.eccen.lh.imag.nii.gz --s

Re: [Freesurfer] rtview - loading a tcl file

Unfortunately it is not working. My command is like this: rtview --s SUBJ --real real.nii --imag imag.nii --eccen --hemi lh --fsig fsig.nii --flat --ss 0 --tcl rtv.tcl rtv.tcl (attached to this email) has just 2 lines as below: labl_remove_all set colscale 8 Thanks

Re: [Freesurfer] rtview - loading a tcl file

What is the tksurfer command that is output? On 7/17/2020 1:13 PM, Nasr, Shahin,Ph.D. wrote: Unfortunately it is not working. My command is like this: rtview --s SUBJ --real real.nii --imag imag.nii --eccen --hemi lh --fsig fsig.nii --flat --ss 0 --tcl rtv.tcl rtv.tcl (attached to this email

Re: [Freesurfer] rtview - loading a tcl file

tksurfer SUBJ lh inflated -aparc -tcl /usr/local/freesurfer/dev/lib/tcl/eccen-flat.tcl as you can see rtv.tcl is dropped. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Friday, July 17, 2020 1:22 PM To: freesurfer@nmr.mgh.har

[Freesurfer] Motor Cortex Label/Mask

External Email - Use Caution Hi, I was wondering if there is a way to extract the whole motor cortex (not the separate regions of the motor cortex, but all of these regions together) of a subject following running recon-all on the subject. Thank you, Anja

Re: [Freesurfer] rtview - loading a tcl file

sorry, they again On 7/17/2020 1:27 PM, Nasr, Shahin,Ph.D. wrote: tksurfer SUBJ lh inflated -aparc -tcl /usr/local/freesurfer/dev/lib/tcl/eccen-flat.tcl as you can see rtv.tcl is dropped. *From:* freesurfer-boun...@nmr.m

Re: [Freesurfer] rtview - loading a tcl file

the tksurfer look correct as below tksurfer SUBJ lh inflated -aparc -tcl /usr/local/freesurfer/dev/lib/tcl/eccen-flat.tcl -tcl rtv.tcl But, eccen-flat.tcl is not executed and I have a blank inflated map. When I drop --tcl rtv.tcl, everything works. From: frees

Re: [Freesurfer] FreeSurfer 7.1 patch question

The tentative date was today, but this morning someone found a bug, and I'd like to get the fix into 7.1.1 On 7/17/2020 1:05 PM, Dincer, Aylin wrote: External Email - Use Caution Hi FreeSurfer Experts, Is there a tentative date when the FreeSurfer 7.1 patch and docker implementatio

Re: [Freesurfer] Motor Cortex Label/Mask

what do you mean by "extract"? In the volume? the surface? or just compute the volume of it? How are you defining motor cortex? On 7/17/2020 1:29 PM, Anja Samardzija wrote: External Email - Use Caution Hi, I was wondering if there is a way to extract the whole motor cortex (not the

Re: [Freesurfer] rtview - loading a tcl file

OK, try again:) On 7/17/2020 1:42 PM, Nasr, Shahin,Ph.D. wrote: the tksurfer look correct as below tksurfer SUBJ lh inflated -aparc -tcl /usr/local/freesurfer/dev/lib/tcl/eccen-flat.tcl -tcl rtv.tcl But, eccen-flat.tcl is not executed and I have a blank inflated map.  When I drop --tcl rtv

Re: [Freesurfer] rtview - loading a tcl file

now the tksurfer command is like this: tksurfer SUBJ lh inflated -aparc -tcl /usr/local/freesurfer/dev/lib/tcl/eccen-flat.tcl -tcl rtview.229508.tcl and rtv.tcl is not applied. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent:

Re: [Freesurfer] Motor Cortex Label/Mask

External Email - Use Caution Hi, I am referring to the anatomical region of interest - the surface. The way that we are able to label the Left-Putamen for example, I would like to be able to label the whole motor cortex. The motor cortex should include the primary motor cortex, pr

Re: [Freesurfer] nu_correct error {Disarmed}

External Email - Use Caution Hi Douglas, I am using the following: Linux Redhat version 7.9 Singularity version 3.6.0 Freesurefer version 6.0.0-min (for containers) I checked all the recon-all.log, and it looks like all of the old reports and I could not find where the error re

Re: [Freesurfer] Cortical Parcellations in FreeDurger 7

External Email - Use Caution Hi Douglas, I see the CLUT file, it's the same one I've been using. I have been using FSL (fslmaths) to extract anatomical ROIs from the aparc+aseg using the CLUT indices as thresholds. This normally works, but results in empty ROIs for thalamic nuclei

Re: [Freesurfer] mri_fieldsign error

No, it does not. The only other problem I can think of is that it has something to do with WSL. Do you have a real linux box you can try it on? On 7/17/2020 5:24 PM, Xiaomin Yue wrote: External Email - Use Caution HI Doug, Sorry for the slow response.  I got the same “segmentation fa

Re: [Freesurfer] mri_fieldsign error

External Email - Use Caution Yes. I will try it on a real Linux box and let you know. Thanks, Xiaomin From: Douglas N. Greve Sent: Friday, July 17, 2020 5:32 PM To: Xiaomin Yue; Freesurfer support list

[Freesurfer] Right and left on MRI scan and on images

External Email - Use Caution Hello, I have an MRI sample collected on a Siemens Magnetom Spectra 3T scanner. However, we do not place any pointing devices inside the scanner to indicate which side is the right and which is the left. I was wondering how the images were acquired - f