Hi Stefano, I think I found and fixed the problem. Can you try these?
On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:
External Email - Use Caution
Hi Doug,
The raw functional file is firstly passed with motion correction (i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering. Next, I have renamed the ICA filtered file as f.nii.gz. Then, I run:
preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 -fsd rest -per-run -sliceorder even -force
There are issues with labels since excluding motion correction doesn't produce key files necessary for concatenating the files. The preprocessing script is searching for the fmcpr.nii.gz file, which cannot be found because it is not created using the -nomc option.
When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and rerun preproc, the operation is done and the fmcpr.odd.sm0.fsaverage.lh is created.
However, when I run the next steps (fcseed-sess -s ID -cfg wm.config -overwrite), a second error occurs (reported below) because the script searches for fmcpr, which cannot be produced since I used -mc.
ERROR: could not determine file for /Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr This error seems to be related to the script searching for the fmcpr file, which isn't available due to the use of -mc.
Thank you.
Best regards,
Stefano
Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi sdellipizzi@gmail.com ha scritto:
Hi Doug have you any news Thank you very much! Stefano
Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi sdellipizzi@gmail.com ha scritto:
Thank you. I’m attaching the file. Stefano <preproc-sess>
Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
can you send me this file /Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess
On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote:
External Email - Use Caution
It seems to me that I've done what you suggest. Attached is a new outputs. Thanks Stefano
Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
Are you sure that you are using the new version that I gave you? It looks like the previous version. Also, it does not look like the entire terminal output.
On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote: > > External Email - Use Caution > > The entire terminal output is attached. > Thanks! > >> Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve >> dgreve@mgh.harvard.edu ha scritto: >> >> entire terminal output >
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline https://secure-web.cisco.com/1jYq_7i1WV2KuJNwpF_8LuUmEt1uXm4GShRtNXC1xe4Y_Bcgi7ubGv5tYLWaiMMMvai3kMGIy815rdOHCuxa26TgzCG7N39_7gO7R1qweyEpbyWhg2jPzT7Jn6y5R9IDYEnulWkwidyb-Qib5lu4h6a_s5YcAdb0N9IiBeDpqWrbBe0hv15Vk8W8n6xL2cuFQJvTXex04uH4CPIgZEpJ6hpPWv7aOcOY-RxxGp_lf2-1SdLn_S3KEKrLQ68nS_U4WOd-L3Q1TxZnV8azAM2dMdrMpcc6aFGCMa7ROC27axgF_fs3uFwdABdIGbgPRYiaC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
External Email - Use Caution
Thank you Doug. The preproc-sess command line runs fine. An error occurs on: fcseed-sess -s ID -cfg wm.config -overwrite ERROR: could not determine file for rs-fMRI_AROMA/ID/rest/001/fmcpr
Best regards Stefano
Il giorno 19 mar 2024, alle ore 15:54, Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
Hi Stefano, I think I found and fixed the problem. Can you try these?
On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:
External Email - Use CautionHi Doug,
The raw functional file is firstly passed with motion correction (i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering. Next, I have renamed the ICA filtered file as f.nii.gz. Then, I run:
preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 -fsd rest -per-run -sliceorder even -force
There are issues with labels since excluding motion correction doesn't produce key files necessary for concatenating the files. The preprocessing script is searching for the fmcpr.nii.gz file, which cannot be found because it is not created using the -nomc option.
When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and rerun preproc, the operation is done and the fmcpr.odd.sm0.fsaverage.lh is created.
However, when I run the next steps (fcseed-sess -s ID -cfg wm.config -overwrite), a second error occurs (reported below) because the script searches for fmcpr, which cannot be produced since I used -mc.
ERROR: could not determine file for /Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr This error seems to be related to the script searching for the fmcpr file, which isn't available due to the use of -mc.
Thank you.
Best regards,
Stefano
Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi <sdellipizzi@gmail.com mailto:sdellipizzi@gmail.com> ha scritto:
Hi Doug have you any news Thank you very much! Stefano
Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi <sdellipizzi@gmail.com mailto:sdellipizzi@gmail.com> ha scritto:
Thank you. I’m attaching the file. Stefano <preproc-sess>
Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> ha scritto:
can you send me this file /Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess
On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote:
External Email - Use CautionIt seems to me that I've done what you suggest. Attached is a new outputs. Thanks Stefano
> Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> ha scritto: > > Are you sure that you are using the new version that I gave you? It looks like the previous version. Also, it does not look like the entire terminal output. > > On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote: >> External Email - Use Caution >> >> The entire terminal output is attached. >> Thanks! >> >>> Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> ha scritto: >>> >>> entire terminal output >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1sSUGeb2ig2jpdimRxpnmJD_858yb00GE2-WzBCOa7CcQFf... https://secure-web.cisco.com/1SN1YTq89Gl2Yc9Gc35qbcP1zY7Yzk8nrFd_WJi-eJvBPKRvK1cbu3ePZQPCtc083GcOammzmc9KqpA7mgrpz-PY7XVwv1f8__96lUkkvm19di852avk-9Myl75ogSo7kvljHKFssCGTebbjiDGGnt8ZV04APBfePwGxReDAjac1msmRvlO370UHrjTiHBMs4EZEi9j8KVDYV5uXqLWrVZBUfBYqD9sDuANCM_pvCfq2HeAo1bNv7WQbVKZs4tT5yuwlZxz53thivcxdfxh-R_26BMJ4CoxbHPhtm0dxZtFMZdYMged3HVDCcTGS_Y07S/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/19VAVeGTK_0MwuD_e9Lge1KBTUyFgZiB_0wQtNJdmJyQ5Pz... https://secure-web.cisco.com/1jYq_7i1WV2KuJNwpF_8LuUmEt1uXm4GShRtNXC1xe4Y_Bcgi7ubGv5tYLWaiMMMvai3kMGIy815rdOHCuxa26TgzCG7N39_7gO7R1qweyEpbyWhg2jPzT7Jn6y5R9IDYEnulWkwidyb-Qib5lu4h6a_s5YcAdb0N9IiBeDpqWrbBe0hv15Vk8W8n6xL2cuFQJvTXex04uH4CPIgZEpJ6hpPWv7aOcOY-RxxGp_lf2-1SdLn_S3KEKrLQ68nS_U4WOd-L3Q1TxZnV8azAM2dMdrMpcc6aFGCMa7ROC27axgF_fs3uFwdABdIGbgPRYiaC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline https://secure-web.cisco.com/19VAVeGTK_0MwuD_e9Lge1KBTUyFgZiB_0wQtNJdmJyQ5Pz7G9Qzu06HKJe_TQNblI_rTEgsefznJY_Mv2nn5SAOCFfifoqeVafVaF0xfn7KdgFSuhX1tSPv_xNheB6sOj_FHFmVbXpyyzlPlVQv4K34ssoCmGdsznLPw5vunmHF_z8m3E4Cc0lBsBisF4cV8G87EAGZDbRpLRtFargovc2nJK3KJvnm1aBq8nHqJIZDUX1kzMyYVwx4BHzs6n8MxUlAKS9ArrHGeCKKNCtQsv_rQ90Cn4tHCLzzp1vpMZkBCkKyMRTWPvWbmouXY2p1C/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline https://secure-web.cisco.com/1jYq_7i1WV2KuJNwpF_8LuUmEt1uXm4GShRtNXC1xe4Y_Bcgi7ubGv5tYLWaiMMMvai3kMGIy815rdOHCuxa26TgzCG7N39_7gO7R1qweyEpbyWhg2jPzT7Jn6y5R9IDYEnulWkwidyb-Qib5lu4h6a_s5YcAdb0N9IiBeDpqWrbBe0hv15Vk8W8n6xL2cuFQJvTXex04uH4CPIgZEpJ6hpPWv7aOcOY-RxxGp_lf2-1SdLn_S3KEKrLQ68nS_U4WOd-L3Q1TxZnV8azAM2dMdrMpcc6aFGCMa7ROC27axgF_fs3uFwdABdIGbgPRYiaC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
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<preproc-sess.txt><rawfunc2surf-sess.txt><rawfunc2tal-sess.txt>
What is your fcseed-config command line? If the input is not fmcpr, then you have to set the input when you config, eg, -funcstem f.even
On 3/19/2024 11:37 AM, Stefano Delli Pizzi wrote:
External Email - Use Caution
Thank you Doug. The preproc-sess command line runs fine. An error occurs on: fcseed-sess -s ID -cfg wm.config -overwrite ERROR: could not determine file for rs-fMRI_AROMA/ID/rest/001/fmcpr
Best regards Stefano
Il giorno 19 mar 2024, alle ore 15:54, Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
Hi Stefano, I think I found and fixed the problem. Can you try these?
On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:
External Email - Use Caution
Hi Doug,
The raw functional file is firstly passed with motion correction (i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering. Next, I have renamed the ICA filtered file as f.nii.gz. Then, I run:
preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 -fsd rest -per-run -sliceorder even -force
There are issues with labels since excluding motion correction doesn't produce key files necessary for concatenating the files. The preprocessing script is searching for the fmcpr.nii.gz file, which cannot be found because it is not created using the -nomc option.
When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and rerun preproc, the operation is done and the fmcpr.odd.sm0.fsaverage.lh is created.
However, when I run the next steps (fcseed-sess -s ID -cfg wm.config -overwrite), a second error occurs (reported below) because the script searches for fmcpr, which cannot be produced since I used -mc.
ERROR: could not determine file for /Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr This error seems to be related to the script searching for the fmcpr file, which isn't available due to the use of -mc.
Thank you.
Best regards,
Stefano
Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi sdellipizzi@gmail.com ha scritto:
Hi Doug have you any news Thank you very much! Stefano
Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi sdellipizzi@gmail.com ha scritto:
Thank you. I’m attaching the file. Stefano <preproc-sess>
Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
can you send me this file /Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess
On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote: > > External Email - Use Caution > > It seems to me that I've done what you suggest. Attached is a > new outputs. > Thanks > Stefano > >> Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve >> dgreve@mgh.harvard.edu ha scritto: >> >> Are you sure that you are using the new version that I gave >> you? It looks like the previous version. Also, it does not look >> like the entire terminal output. >> >> On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote: >>> >>> External Email - Use Caution >>> >>> The entire terminal output is attached. >>> Thanks! >>> >>>> Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve >>>> dgreve@mgh.harvard.edu ha scritto: >>>> >>>> entire terminal output >>> >> >> _______________________________________________ >> 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 this e-mail was sent >> to you in error and the e-mail contains patient information, >> please contact the Mass General Brigham Compliance HelpLine at >> https://www.massgeneralbrigham.org/complianceline >> https://www.massgeneralbrigham.org/complianceline . >
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline https://secure-web.cisco.com/1jYq_7i1WV2KuJNwpF_8LuUmEt1uXm4GShRtNXC1xe4Y_Bcgi7ubGv5tYLWaiMMMvai3kMGIy815rdOHCuxa26TgzCG7N39_7gO7R1qweyEpbyWhg2jPzT7Jn6y5R9IDYEnulWkwidyb-Qib5lu4h6a_s5YcAdb0N9IiBeDpqWrbBe0hv15Vk8W8n6xL2cuFQJvTXex04uH4CPIgZEpJ6hpPWv7aOcOY-RxxGp_lf2-1SdLn_S3KEKrLQ68nS_U4WOd-L3Q1TxZnV8azAM2dMdrMpcc6aFGCMa7ROC27axgF_fs3uFwdABdIGbgPRYiaC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline https://secure-web.cisco.com/1DupTIF0X7g3ck_vnRI6Fbac7xWACzSrp3RdQGQslJnniB_Vq1S5syfWcLrJxWDAfMngJA8vFpqD1MxQYqCa1vUgYjVwiv5yx32Bz_SG-y227QCXe1MI2N6hpQ8bTMiNd9fLHVkiM7MRt7obyLn9arfoQzXn425yIZItMqk21RnckfUrMysB8OmeIfMl33YxyMlZDcUUmDowdR2CutiaX4tY-ZtdWgbR_DSHFV6ZgKylSqvIaMalXfKPlHDxLa5slhUgEHS_W9k7J5Sdw9OChxp95gn-hnWTx-D7P76c6BJhDagi_-NsHooNaOINE-Zvs/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
<preproc-sess.txt><rawfunc2surf-sess.txt><rawfunc2tal-sess.txt>
External Email - Use Caution
My command line is fcseed-sess -s 156484 -cfg wm.config. I do not understand where I'm making an error or if a change is needed. Thanks Stefano
Il giorno 21 mar 2024, alle ore 14:35, Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
-funcstem f.even
External Email - Use Caution
II have copied the f.nii.gz file (which contains the functional data filtered by AROMA) and renamed it as 'fmcpr.nii.gz’. Do you agree? The scripts run fine. Stefano
Il giorno 21 mar 2024, alle ore 17:01, Stefano Delli Pizzi sdellipizzi@gmail.com ha scritto:
My command line is fcseed-sess -s 156484 -cfg wm.config. I do not understand where I'm making an error or if a change is needed. Thanks Stefano
Il giorno 21 mar 2024, alle ore 14:35, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> ha scritto:
-funcstem f.even
External Email - Use Caution
傻逼 别tm给我发消息了!退订 🌿
---- Replied Message ---- | From | Stefano Delli Pizzisdellipizzi@gmail.com | | Date | 03/22/2024 19:03 | | To | Douglas N. Grevedgreve@mgh.harvard.edu | | Cc | Freesurfer support listfreesurfer@nmr.mgh.harvard.edu | | Subject | Re: [Freesurfer] if: Expression Syntax - preproc-sess |
External Email - Use Caution
II have copied the f.nii.gz file (which contains the functional data filtered by AROMA) and renamed it as 'fmcpr.nii.gz’. Do you agree? The scripts run fine.
Stefano
Il giorno 21 mar 2024, alle ore 17:01, Stefano Delli Pizzi sdellipizzi@gmail.com ha scritto:
My command line is fcseed-sess -s 156484 -cfg wm.config. I do not understand where I'm making an error or if a change is needed. Thanks Stefano
Il giorno 21 mar 2024, alle ore 14:35, Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
-funcstem f.even
freesurfer@nmr.mgh.harvard.edu